Modular antigen transportation molecules and uses therof

ABSTRACT

The present invention relates to (isolated) recombinant proteins, also referred to as improved MAT (iMAT) molecules, comprising at least one translocation module, at least one targeting module and at least one antigen module, wherein at least one cysteine residue is substituted with a different amino acid residue. Such iMAT molecules are useful specifically as vaccines, e.g., for therapy and/or prevention of allergies and/or infectious diseases and/or prevention of transmission of infectious diseases in equines. The present invention further relates to nucleic acids encoding such iMAT molecules, corresponding vectors and primary cells or cell lines.

SEQUENCE LISTING

This application contains a sequence listing in accordance with 37 C.F.R. 1.821-1.825. The sequence listing accompanying this application is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to (isolated) recombinant proteins, also referred to as improved MAT (iMAT) molecules, comprising at least one translocation module, at least one targeting module and at least one antigen module, wherein at least one cysteine residue is substituted with a different amino acid residue. The iMAT molecules may be produced with substantially reduced manufacturing efforts and are species-specific, safer and immunologically very effective. Such (isolated) recombinant proteins are useful specifically as vaccines, e.g., for therapy and/or prevention of allergies and/or infections and/or prevention of transmission of infections in equines.

BACKGROUND OF THE INVENTION

The processing of antigens by antigen-presenting cells (APCs) takes place by two different routes. Antigens occurring inside the cell are presented by MHC I (major histocompatibility complex class I, MHC class I) molecules on the cell surface, whereas extracellular antigens are presented by MHC II (major histocompatibility complex class II, MHC class II) molecules on the cell surface. Both mechanisms initiate an immune response by the host to the antigen. The route taken by the antigen from uptake into the cell until presentation on the cell surface in the form of an MHC II-antigen complex proceeds via various cell organelles, inter alia via the endoplasmic reticulum, the Golgi apparatus, the trans-Golgi network, lysosomes, endosomes and via MHC class II compartments (MIICs). The MIICs play an important part in the MHC II-mediated antigen presentation. In these organelles of the cell, the MHC II molecules are loaded with low molecular weight antigens or with proteolytic fragments of proteins. In this process, the invariant chain (also called MHC II gamma chain or Ii) which is initially bound to the MHC II molecule undergoes proteolytic degradation, and the antigen is bound to the MHC II molecule under the regulation of various proteins which bind directly or indirectly to MHC II. These regulatory molecules in humans include, inter alia HLA-DM, HLA-DO, LAMP-1, LAMP-2, CD63, CD83, etc. The exact function of these proteins is in part unexplained as of yet, but many of them have signal sequences which promote their transport to the lysosomes, to the endosomes, to the trans-Golgi network, to the MIICs, etc. A number of proteases are involved in the proteolytic processing necessary, so that the antigen can be presented on MHC II molecules. The proteases present in MIICs include, inter alia various members of the cathepsin family such as, for example, cathepsin S and cathepsin L. In species other than humans, the homologue MHC Class II molecules have different amino acid sequences. In Equine animals the organization of the MHC system is similar to humans with contiguous class I, III, and II regions (Kelley J et al., Immunogenetics 2005, 56: 683-695).

The concept of providing modular antigen transportation (MAT) molecules for modulating immune responses, associated constructs, method and uses thereof is disclosed in WO 2004/035793 (US equivalent US 2005/0281816), hereby incorporated by reference. This document describes the usefulness of a three-part-molecule, the MAT molecule, for introducing epitopes of antigens into cells, thus, determining the immune response to be modulated by such MAT molecule. Therein, various translocation modules, targeting modules as well as antigen modules are described. This technology and its underlying method make it possible, firstly, to convey antigens efficiently from the extracellular space into the intracellular space of a target cell, and, secondly, make it possible for the antigens, after arrival in the interior of the cell, to reach efficiently cell organelles in order to be subsequently processed for antigen presentation. Generally, the two-stage process can be utilized for the targeted, efficient modulation of the immune response in a subject. The use of MAT molecules is disclosed for example in Martínez-Gómez J M et al. [Allergy 2009, 64(1): 172-178]; Rose H (Arb Paul Ehrlich Inst Bundesinstitut Impfstoffe Biomed Arzneim Langen Hess, 2009, 96, 319-327) as well as recently in Senti G et al. [J Allergy Clin Immunol., 2012, 129(5): 1290-1296]. Based on the MAT technology, the major cat allergen Fel d1 was fused to a TAT-derived protein translocation domain and to a truncated invariant human chain for targeting the MHC class II pathway. Immunogenicity was evaluated in mice, while potential safety issues were assessed by suitable tests based on basophil reactivities from cat-dander-allergic patients. The possible use of this model compound has been demonstrated. It is described therein, that it is expected that MAT molecules are safer and more efficient in inducing the desired immune response, namely hyposensitization, than recombinant allergens or allergen extracts in conventional allergen-specific immunotherapy (SIT). In the recent publication by Senti G. et al. intralymphatic immunotherapy for cat dander allergy in humans inducing tolerance after three injections was described. Therein, a first-in-human clinical study with the MAT-Fel d1 was described, demonstrating safety and induction of allergen tolerance after intra-lymphatic injection of three injections only.

Further prior art is as follows:

Gadermaier G et al. (Molecular Immunology 2010, 47: 1292-1298) describe the targeting of the cysteine-stabilized fold of Art v1 for immunotherapy of Artemisia pollen allergy. The authors used genetic engineering approaches for targeting Art v1 posttranslational modifications aiming at the creation of hypoallergenic molecules: (i) disulfide bridges of the defensin domain were disrupted by site-directed mutagenesis and (ii) the mutant constructs expressed in E. coli for the production of non-glycosylated proteins. However, the objective was clearly only manipulating the three-dimensional fold of the Art v1 defensin domain to abrogate IgE-binding (i.e. creating a hypoallergenic molecule) by exchanging single cysteine residues for serine—while keeping intact (i.e. unmodified) the recognized T-cell epitopes (even if such contain cysteine residues).

The report of the 3^(rd) Havemeyer workshop on allergenic diseases of the Horse (Hólar, Iceland, June 2007, Veterinary Immunology and Immunotherapy 2008, 126: 351-361) focused on immunological and genetic aspects of insects bite hypersensitivity (IBH) and recurrent airway obstruction (RAO). At this workshop, novel approaches for SIT against IBH were discussed, among others, the use of viral vectors or protein vaccination with allergens coupled to modular antigen translocating (MAT) molecules.

In SIAF Annual Reports 2010 and 2011 Crameri R reports the use of MAT technology for vaccination of IBH-affected horses.

However, major problems arose when producing and manufacturing the MAT molecules described in the prior art. In particular standard methods used in developing a downstream process (DSP) for manufacturing of the MAT molecules under good manufacturing practice (GMP) could not be applied. It was not possible to purify a homogeneous molecular species of the MAT molecules, evidently due to their anomalous physicochemical properties.

Several methods of purification could not be applied (see Example 5 herein) with the MAT molecules described in the prior art although different separation principles (e.g., size exclusion chromatography, RP-HPLC) were tested. Methods applied for determination of purity for recombinant proteins in general include chromatographic separation, e.g., RP-HPLC and electrophoretic separation (e.g. capillary zone electrophoresis, isoelectric focusing, SDS-PAGE under reducing or non-reducing conditions). Also, these analytical methods could not be applied on MAT molecules without molecule-specific adaptations. For the assessment of purity, an adapted specific SDS-PAGE test procedure had to be developed. This test procedure includes sample preparation with reducing agent and lithium dodecyl sulfate (LDS) and heating up to 75° C., resulting in multiple, reproducible sharp bands after electrophoretic separation. Staining with Coomassie blue dye leads to linear quantitative behavior (densitometry) in gels. Using a monoclonal antibody that allows for detection of the allergen module in a MAT molecule exhibited a main band and several minor bands. All bands migrate reproducibly to the same position as in the original gel also after re-loading a second gel with excised bands of the first gel. Surprisingly, in all of these bands with apparent lower and higher molecular weight, the full length MAT molecules were identified by excision of bands out of the gel, their tryptic digestion and subsequent analysis by mass spectrometry (nanoLC/ESI-MS-MS). From these experiments an untypical, anomalous behavior of different folding variants of MAT molecules in the SDS-PAGE can be concluded (“gel shifting”). Furthermore, in all batches of MAT molecules multimeric forms of the protein could be detected which were difficult to separate from monomeric forms.

For e.g. economic aspects, but also for regulatory requirements, it is necessary to improve (i) the manufacturing process of the MAT molecules and (ii) their suitability for standard analytical methods of purity determination. Additionally, for adapting the MAT molecules to specific target species, such as equines, adaption of the immunological targeting within the MAT technology is required.

Additionally, the MAT molecules are readily employed in allergies elicited by a known major allergen (e.g., cat dander allergy in humans by Fel d1). However, it seems difficult to employ the MAT molecules of the prior art in clinical settings, such as allergies, where for instance a variety of non-cross-reactive allergens are known to be involved, but the importance of such allergens in eliciting the allergy is unknown (i.e. the major allergens are unknown).

The objective underlying the invention is to provide improved MAT molecules useful as active agents in pharmaceutical composition, such as vaccines, which overcome the problems of the prior art.

DISCLOSURE OF THE INVENTION Summary of the Invention

In one aspect, the objective underlying the invention has surprisingly been solved by providing a(n) (isolated) recombinant protein, preferably an improved MAT (iMAT) molecule, comprising:

-   -   i. at least one first module being an amino acid sequence         allowing the translocation of the iMAT molecule from the         extracellular space into the interior of cells,     -   ii. at least one second module being an amino acid sequence         allowing species-specific intracellular targeting of the iMAT         molecule to the cell organelles which are involved in the         processing of antigens and/or the loading of MHC molecules with         antigens, preferably processed antigens, and     -   iii. at least one third module as antigen module being an amino         acid sequence derived from at least one full or partial epitope         of at least one antigen, preferably at least one allergen,         determining the specificity of an immune response modulated by         such iMAT molecule,         characterized in that at least in the antigen module(s) at least         one cysteine residue is substituted with a different amino acid         residue, preferably serine, leucine, isoleucine and/or aspartic         acid.

Preferably, in the at least one antigen module all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine and/or aspartic acid. More preferably in the entire iMAT molecule all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine and/or aspartic acid.

Preferably, if not all cysteine residues are substituted with a different amino acid residue, preferably serine, leucine, isoleucine and/or aspartic acid, an even number of cysteine residues remains in the entire iMAT molecule.

Preferably, all of such modules are covalently linked to each other, optionally by additional spacer module(s) between two or more adjacent, optionally all, of such first, second and/or third modules.

More preferably, all of such modules are covalently linked to each other and no additional spacer module(s) are present between two or more adjacent modules of such first, second and/or third modules at all.

In another aspect, the objective underlying the invention has surprisingly been solved by providing a vaccine or immunogenic composition or pharmaceutical composition comprising the (isolated) recombinant protein as herein disclosed and claimed.

In another aspect, the objective underlying the invention has surprisingly been solved by providing the (isolated) recombinant protein as herein disclosed and claimed or the vaccine or immunogenic composition or pharmaceutical composition as herein disclosed and claimed for use in a method of prevention and/or therapy of one or more allergies in equines, preferably insect bite hypersensitivity (IBH), urticaria and/or recurrent airways obstruction (RAO). Corresponding methods of prevention and/or treatment of equines in need thereof and uses for the preparation of a pharmaceutical composition/medicament for the prevention and/or treatment of equines are also intended to be within the scope of the present invention.

In another aspect, the objective underlying the invention has surprisingly been solved by providing the (isolated) recombinant protein as herein disclosed and claimed or the vaccine or immunogenic composition or pharmaceutical composition as herein disclosed and claimed for use in a method of prevention and/or therapy of one or more infectious diseases in equines and/or prevention of transmission of one or more infectious diseases in equines and/or prevention of transmission of one or more infectious diseases in equines by vectors, preferably by blood feeding flies, midges, ticks and/or mosquitos, more preferably rhodoccus pneumonia, strangles, African horse sickness, West Nile Virus infection, dermatophytosis and/or parasites of the digestive tract and/or other organs and/or cryptosporidiosis, helminths and/or their prepatent stages. Corresponding methods of prevention and/or treatment of equines in need thereof and uses for the preparation of a pharmaceutical composition/medicament for the prevention and/or treatment of equines are also intended to be within the scope of the present invention.

In a further aspect, the objective underlying the invention has surprisingly been solved by providing a nucleic acid encoding the (isolated) recombinant protein as herein disclosed and claimed.

In a further aspect, the objective underlying the invention has surprisingly been solved by providing a vector comprising at least one nucleic acid as herein disclosed and claimed.

In yet a further aspect, the objective underlying the invention has surprisingly been solved by providing a primary cell or cell line comprising at least one nucleic acid as herein disclosed and claimed and/or at least one vector as herein disclosed and claimed.

Surprisingly, the iMAT molecules according to the present invention, as herein disclosed and claimed, do possess physicochemical and/or immunological characteristics that render them superior to the MAT molecules of the pertinent prior art:

-   -   i. The substitution of at least one cysteine residue, preferably         all cysteine residues, with a different amino acid residue in         the antigen module(s), preferably entire iMAT molecule, which         was selected in silico not to compromise the stability of the         final iMAT molecule, renders the iMAT molecule according to the         present invention surprisingly suitable for the application of         standard purification procedures for biopharmaceuticals as well         as for standard analytical methods.     -   ii. The preferred direct covalent linkage of the modules of the         iMAT molecule, i.e., first translocation module, second         targeting module and third antigen module, without any         additional spacer modules between such modules, i.e., no         additional spacer modules between two or more adjacent modules         of such first, second and/or third modules at all, contributes         in addition to (i) the superior characteristics of the iMAT         molecules according to the present invention: such iMAT         molecules which are thought to be more rigid in         three-dimensional structure and hence unable to form         conformational IgE epitopes, are even more         hypoallergenic—virtually no allergenicity could be detected as         shown in Example 2 herein.     -   iii. The preferred presence of a(n) (quasi) N-terminal His-tag         results in iMAT molecules according to the present invention         that can be used as surrogate markers for monitoring immunity         and/or duration of immunity since such tag module, optionally         together with one or more adjacent amino acid residues from the         translocation module, can be used to induce a specific         immunologically detectable signal (e.g. an antibody) in the         target subject, that is specific to the generic structure of the         iMAT molecules (see Example 1 herein). Additionally, the         presence of such tag module can be used for separating proteins         in a sample comprising the iMAT molecules according to the         present invention, e.g. using zinc- or cobalt-charged solid         supports, and hence further improves the possibility to produce         iMAT molecules according to the present invention without         aggregation during the purification process.     -   iv. The at least one targeting module in the iMAT molecules         according to the present invention preferably is         species-specific, i.e. in case of an intended application of         such iMAT molecules to equines an equine targeting module, e.g.         the equine invariant chain, is chosen. By this species-specific         targeting optimized binding characteristics of the iMAT         molecules according to the present invention to the MHC Class II         molecules can successfully be achieved.     -   v. The at least one antigen module in the iMAT molecules         according to the present invention is preferably an allergen.         This could be derived from mold (fungi and/or their spores),         pollen, house dust or forage mites (and/or their feces),         preferably pollen from tree, grass, herbaceous, ambrosia and/or         brassicaceae pollen and/or fungi and/or their spores of the         genera aspergillus, alternaria, botrytis, cercospora,         cladosporium, curvularia, drechslera, eurotium,         helminthosporium, epicoccum, erysiphe/oidium, fusarium,         lichtheimia, nigrospora, penicillium, periconia, peronospora,         polythrincium, saccharopolyspora (formerly also faenia or         micropolyspora), thermoactinomyces, stemphylium, torula and/or         mites (or their feces) of the genera acarus, glycophagus,         tyrophagus, dermatophagoides. The at least one antigen module in         the iMAT molecules according to the present invention is more         preferably a culicoides allergen. The allergen was selected         according to the following criteria: when major allergens         eliciting an allergy in subjects are unknown, the at least one         antigen module in the iMAT molecules according to the present         invention can be selected by a bioinformatics approach as         described exemplarily and in detail in Examples 6 and 7 herein.         By this means improved MAT molecules can be achieved which are         useful specifically as vaccines, e.g. for therapy and/or         prevention of allergies in equines. The at least one antigen         module in the iMAT molecules according to the present invention         may also be an antigen of a pathogen involved in one or more         infectious disease(s). This could be derived from the genera         rhodococcus, streptococcus, orbivirus, flavivirus, trichophyton,         microsporum, cryptosporidium and/or strongylus. The at least one         antigen module in the iMAT molecules according to the present         invention may also be an antigen of a vector involved in the         transmission of one or more infectious disease(s), e.g.         culicoides, culex and/or ixodes saliva components. By this means         improved MAT molecules can be achieved which are useful         specifically as vaccines, e.g. for therapy and/or prevention         and/or prevention of transmission of infectious diseases in         equines.

In particular, the present invention provides (isolated) recombinant proteins exhibiting an improved solubility, that are readily applicable to chromatographic separation techniques and that show an improved stability.

In addition, the (isolated) recombinant proteins according to the present invention preferably display high activities and efficacies in inducing the desired immunological effects, namely, advantageously species specific modulating the immune response against allergens in a subject, preferably an equine. By this means treatment and amelioration of symptoms of IBH affected equines becomes feasible.

DETAILED DESCRIPTION OF THE INVENTION

Before the embodiments of the present invention are described in further details it shall be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. All given ranges and values may vary by 1 to 5% unless indicated otherwise or known otherwise by the person skilled in the art, therefore, the term “about” was usually omitted from the description and claims. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing the substances, excipients, carriers, and methodologies as reported in the publications which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

The terms “isolated recombinant protein”, “recombinant protein” and/or “improved MAT (iMAT) molecule” are interchangeably used in the course of the present invention. They all have the identical meaning.

The term “module” in the course of the present invention refers to a specific amino acid sequence, e.g. a part, a unit or a moiety of a polypeptide, usually short amino acid/peptide sequences, having a defined function.

The term “first module being an amino acid sequence allowing the translocation of the (isolated) recombinant protein, preferably improved MAT (iMAT) molecule, from the extracellular space into the interior of cells”, herein also interchangeably referred to as “translocation module” or “translocation sequence”, in the course of the present invention refers to a specific amino acid sequence that promotes the transport of the cargo molecule, e.g., amino acid sequence, peptide, polypeptide, protein and other classes of substances, such as nucleic acids or pharmaceutically active ingredients (API), to the interior of cells, in particular eukaryotic cells, more particular, cells expressing the MHC class II molecules on the surface and/or the MHC class I molecules on the surface, as known in the literature.

By the presence of the translocation module it is possible to promote the entry of said cargo molecule into the cells.

Amino acid sequences useful as translocation modules are described in the prior art. For example, U.S. Pat. No. 7,653,866 discloses several useful translocation sequences including the HIV-tat molecule or the protein VP22, which is derived from herpes simplex virus. This principal of promoting the entry of a given target molecule into the interior of cells is described numerously in various studies in the pertinent patent and non-patent literature. In addition, suitable translocation sequences include homeoprotein sequences, leucine zipper sequences, arginine-rich and/or lysine-rich sequences, and various other sequences of proteins or polypeptides which are secreted despite the absence of a secretion signal sequence. Particularly useful are viral peptide sequences, e.g. the protein HIV transcriptional activator protein (HIV tat). The Tat sequence or Tat peptide has been described in the prior art including various modifications. All the variations described in the prior art for peptide sequences of Tat are generally suitable as translocation modules. Other examples include the VP22 peptide as well as antennapedia peptides derived from the drosophila homeotic protein antennapedia. In addition, other homeoproteins may be used. Various examples of suitable homeoproteins are described in the prior art. In addition, leucine zipper proteins, like human cFos-(139-164), or human cJun-(252-279) can be used. Moreover, arginine-rich and/or lysine-rich peptides are suitable as translocation modules including sequences like HIV-1 rev (34-50) or other peptides derived from virus or yeast. Of course, the polyarginine-rich and/or polylysine-rich peptides can be produced synthetically. Said polyarginine-rich and/or polylysine-rich peptides may comprise further amino acids. Suitable examples are described in the pertinent prior art.

In a preferred embodiment, the at least one translocation module comprises, and preferably consists of, an amino acid sequence which does not consist of a complete protein sequence, as illustrated above, but instead of a minimal sequence still being functional, i.e., capable of effectively promoting cell entry. A suitable minimal sequence is, for instance, the amino acid sequence according to SEQ ID NO: 1.

In another preferred embodiment, the at least one translocation module comprises, and preferably consists of, HIV-tat, VP22 and/or Antennapedia or a partial sequence thereof, provided that such at least one translocation module is functional as a module for translocation from the extracellular space into the interior of cells.

The term “second module being an amino acid sequence allowing species-specific intracellular targeting of the (isolated) recombinant protein, preferably improved MAT (iMAT) molecule, to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, preferably processed antigens”, herein also interchangeably referred to as “targeting module” or “targeting sequence”, in the course of the present invention refers to a specific amino acid sequence that allows/promotes the intracellular transport of the (isolated) recombinant proteins, as disclosed and claimed herein, to such cell organelles that are involved in the processing of antigens and/or the loading of MHC molecules with antigens.

In particular, such cell organelles include the endoplasmic reticulum, the Golgi apparatus, the trans-Golgi network, lysosomes, endosomes and MHC II compartments. These intracellular organelles are involved in processes such as, for example, the transport and/or processing of antigens, the preparation and/or loading of MHC II molecules with antigens or processed antigens, and/or the transport of the MHC II molecules loaded with such antigens to the cell surface.

A number of sequences are known in the prior art. A prominent example of useful targeting sequences includes the invariant chain of MHC class II molecules also known as Ii invariant chain or MHC II gamma chain. Various variants of the invariant chain are described in the patent and non-patent literature.

In a preferred embodiment of the present invention, the invariant chain is chosen from the species in which the immune response should be modulated and/or from the species in which the iMAT molecule should be intracellularly targeted.

For example, for equines, such as horses, the preferred invariant chain chosen is the equine invariant chain, comprising, preferably consisting of the amino acid sequence according to SEQ ID NO: 2 or fragments thereof provided such fragments maintain their intracellular transport function. Preferred such fragments are the amino acid sequences according to SEQ ID NOS: 15 and/or 16.

Other suitable examples for targeting sequences include lysosomal membrane proteins, comprising sequences suitable as targeting modules. That are, a number of membrane proteins occurring in lysosomes which have sequence motifs that allow targeting the lysosome. These groups of proteins include inter alia lamp 1, lamp 2, lamp 3, limp II and lap. In addition, tetraspan proteins are known in the prior art as targeting modules. Additional proteins can be found in the endosomal/lysomal compartments that show targeting properties. A skilled person is aware how to determine suitable targeting sequences accordingly.

In another preferred embodiment, the at least one targeting module comprises, and preferably consists of, the equine invariant chain and more preferably consists of one or more of the amino acid sequences of SEQ ID NOS: 2, 15, 16.

The term “third module as antigen module being an amino acid sequence derived from at least one full or partial epitope of at least one antigen, preferably at least one allergen, determining the specificity of an immune response modulated by such (isolated) recombinant protein, preferably improved MAT (iMAT) molecule (in a subject, preferably an equine)”, herein also interchangeably referred to as “antigen module” or “antigen sequence”, in the course of the present invention refers to a specific amino acid sequence that allows modulating the immune response against the epitope/antigen and determining the specificity of the immune response in a subject, preferably an equine.

In this context, such antigen module(s) comprise(s) at least one cysteine residue that is substituted with a different amino acid residue, preferably serine, leucine, isoleucine and/or aspartic acid. Thus, the immune response is different compared to the immune response of a subject, preferably an equine, exposed to the unchanged amino acid sequence of the antigen.

There are no restrictions relating to the antigens on the basis of the method. The method can be used for example for activating the immune system of a subject against pathogens such as, for example, against viruses, bacteria, fungi, parasites, protozoa etc., i.e., very generally as a vaccine. Additionally, the method can be used not only directly against such pathogens, but also to activate the host immune system to prevent the transmission in vector-borne diseases involving viruses, bacteria, fungi, parasites, protozoa, etc. In addition, the method can be used to activate the immune system against degenerated cells such as, for example, tumor cells, etc. However, it can also be used on the other hand for desensitization of the immune system of a subject against allergens such as, for example derived from food, mold (fungi and/or their spores), pollen, animal hair, house dust or forage mites (and/or their feces), insect toxins, etc. or for targeted suppression of the immune system, e.g., if autoimmune reactions are present, such as, for example, arthritis, rheumatism, diabetes, SLE (systemic lupus erythematosus), etc., and for suppressing transplant rejection reactions. Further disorders which are not expressly mentioned and which are associated with an immune reaction which is too strong or too weak can likewise be treated with the iMAT molecules, as disclosed and claimed herein.

It is possible to employ as antigen modules for the purposes of the invention in principle all types of antigens able to modulate an immune response. Both, antigens currently already known and antigens to be discovered in future are suitable. In some circumstances, the antigens may also be those which do not lead to an immune response with conventional immunization methods known in the art at present, but which lead on application of the novel method described in the present invention to an immune response by the subject. Further, the term antigen encompasses antigenic fragments comprising the antigenic determinant/the antigenic determinants which are also known as epitope(s). Thus, the antigen module may be the whole molecule, e.g., the protein, or is a part of the molecule, i.e., a fragment thereof, like a peptide, encompassing at least one antigenic determinant or epitope. The at least one antigenic determinant or epitope is able to elicit an immune response against the antigen. The epitope can comprise one or more than one amino acid or peptide or other structure capable of eliciting an immune response such as sugar structures, phosporylated amino acids, etc., or combinations thereof. The antigen can be a continuous epitope (i.e., not dependent on conformation, e.g., present in for example native and denatured proteins) or a discontinuous epitope (i.e., dependent on conformation, e.g., only present in native, folded, but not present in denatured proteins). It is possible to use not only proteins and peptides, but also sugar structures, lipids, e.g., lipopolysaccharides, lipoteichoic acids and other constituents of bacterial membranes (CD1b binds, for example, sugar structures and lipids), nucleic acids such as, for example, DNA comprising CpG motifs, organic substances such as, for example, latex or pharmaceutically active substances as antigen for the purposes of the present invention. The antigen may be derived from all possible life forms, such as e.g. humans, animals, plants, fungi, parasites, unicellular or multicellular microorganisms, viruses and other life forms. The antigens may have been isolated from biological material, have been prepared as recombinant antigens or have been prepared by synthesis, e.g., by peptide synthesis. Synthetically prepared antigens may be substances which occur in nature or which do not occur in nature but are obtainable by chemical synthesis. Examples of non-naturally occurring substances which are, however, suitable as antigen in some circumstances are, for example, synthetically prepared substances which are present in medicaments, or synthetic peptides having amino acid sequences which do not occur in nature, or peptidomimetics, etc. Naturally occurring or synthetic or recombinant antigens can be modified by molecular biology, enzymatic, chemical and/or other methods in order to confer on them properties which are more advantageous for the particular application. These advantageous properties may be, inter alia, a higher or lower activity as antigen, a broader or a more specific action as antigen, a better solubility in hydrophilic or hydrophobic solvents, a greater permeability of the antigen modules for cell membranes, for membranes of organelles, for the blood-brain barrier, for the blood-CSF barrier etc., a higher or lower half-life in vivo or in vitro, a lower or higher toxicity, a better detectability of the antigen in vivo or in vitro after application of the antigen in the form of an iMAT molecule, etc. It is additionally possible for the purposes of the present invention to combine a plurality of antigens in one antigen module. For this it is possible for identical antigens to be present in more than one copy in the antigen module, or it is possible for example for different variants of the same antigen to be combined in an antigen module. Combination of antigens, e.g. of antigen 1, and other antigens, e.g., of antigen 2, in an antigen module is also possible, etc. Further combinations, such as, for example, antigen 1 in more than one copy and antigen 2 in a single copy may also be combined in an antigen module, etc. It is additionally possible also for one or more different and/or one or more identical antigen modules to be present in an iMAT molecule. It is possible in principle for all possible combinations of singly and multiply present identical or altered copies of antigens derived from one or more different antigen to be combined for the purposes of the invention.

In a preferred embodiment, the antigen module comprises at least one full or partial epitope derived from at least one antigen, wherein such antigen is an allergen. At least one epitope is able to elicit an immune response against the allergen whereby the epitope can comprise one or more than one structure, e.g., a peptide, capable of eliciting an immune response. The epitope may be a continuous epitope or a discontinuous epitope of the allergen. Epitopes are preferably at least of eight amino acids in length, preferably are at least ten amino acids in length, and more preferably at least 13 amino acids in length. The antigen module comprises at least one full or partial epitope, but may also comprise two or more full or partial epitopes which may be identical or different from each other. Further, the antigen module may comprise additional amino acid sequences adjacent to the at least one full or partial epitope. The epitope may be the natural occurring epitope or may be a modified epitope, either modified in its amino acid sequence and/or by one or more post translational modifications.

In an embodiment, the at least one third antigen module comprises at least one full or partial epitope derived from at least one antigen of a pathogen involved in one or more infectious disease(s). This could be derived from the genera rhodococcus, streptococcus, orbivirus, flavivirus, trichophyton, microsporum, cryptosporidium and/or strongylus. The at least one antigen module in the iMAT molecules according to the present invention may also be an antigen of a vector involved in the transmission of one or more infectious disease(s), e.g., culicoides, culex and/or ixodes saliva components.

In a further preferred embodiment, the at least one third antigen module comprises at least one full or partial epitope derived from at least one allergen eliciting one or more allergy(ies) in equines. This could be at least one full or partial epitope of at least one allergen derived from mold (fungi and/or their spores), pollen, house dust or forage mites (and/or their feces), preferably pollen from tree, grass, herbaceous, ambrosia and/or brassicaceae pollen and/or fungi and/or there spores of the genera aspergillus, alternaria, botrytis, cercospora, cladosporium, curvularia, drechslera, eurotium, helminthosporium, epicoccum, erysipheloidium, fusarium, lichtheimia, nigrospora, penicillium, periconia, peronospora, polythrincium, saccharopolyspora (formerly also faenia or micropolyspora), thermoactinomyces, stemphylium, torula and/or mites (or their feces) of the genera acarus, glycophagus, tyrophagus, dermatophagoides

In a preferred embodiment this is, preferably at least one full or partial epitope of at least one allergen derived from blood feeding insects, more preferably from the genus culicoides.

Examples of allergens of the genus culicoides are shown in FIG. 1 identifying the species, the allergen and the uniprot accession number (database release is UniProt release 2013_09).

In a further preferred embodiment, such at least one allergen is Cul n4, Cul 01, Cul o2, Cul o3, Cul o4 and/or Cul o7 allergen. Preferred specific sequences of the antigen modules are the amino acid sequences according to SEQ ID NOS: 3, 4, 5, 6, 18, 19.

The term “immune response modulated by ( . . . )” or interchangeably “immunomodulatory immune response”, in connection with “(isolated) recombinant protein” and/or “iMAT molecule” in the course of the present invention refers to immunogenic and/or tolerogenic immune responses.

The term “allergen” in the course of the present invention refers to a type of antigen that in the native form produces an abnormally vigorous immune response in which the immune system fights off all perceived threats that would otherwise be harmless to the subject. Typically, these kinds of reactions result in the phenotype known as allergy. Various types of allergens are described in the prior art, including foods, drugs, animal products or natural or synthetic material. Preferably, a protein is considered to be an allergen, when it elicits in the native form a specific IgE response in at least five subjects, preferably equines. For the avoidance of doubt, an “allergen” in connection with the “at least one third antigen module comprising at least one full or partial epitope derived from at least one allergen” does not need to be in the native form any longer, which is also preferred—in other words, the term “allergen” in the course of the present invention also explicitly refers to non-native amino acid sequences as part of the iMAT molecules, as described and claimed herein, that do not elicit a specific IgE response in at least five subjects, preferably equines, any longer.

The term “epitope”, herein also interchangeably referred to as “antigenic determinant”, in the course of the present invention refers to the part of an antigen that is recognized by the immune system, either by B-cells or T-cells. Epitopes are presented on the surface of antigen presenting cells by means of MHC molecules to which they are bound.

The term “subject”, herein also interchangeably referred to as “individual” and/or “organism”, in the course of the present invention preferably refers to equines.

The term “equine”, herein also interchangeably referred to as “horse”, in the course of the present invention encompasses any member of the genus Equus. It encompasses, e.g., any horse, pony and/or donkey, the taxonomic designations Equus ferus and/or Equus caballus, and/or the subspecies Equus ferus caballus. The equine may, e.g., be a domestic horse.

The terms “peptide” and “protein” are used side by side as equivalent in the course of the present invention. A peptide or a protein means for the purposes of the present invention a covalent connection of at least two amino acids via a peptide linkage. The term “amino acid” and the term “amino acid residue” are used as equivalents in the present application, i.e., the meaning of the two terms is identical. The terms amino acid/amino acid residue and peptide/protein are used in the present application in the form of the widest possible definition.

In this connection, the term “recombinant protein” refers to a polypeptide which may be obtained by genetic engineering and expression in eukaryotic or prokaryotic systems. In addition, said term encompasses polypeptides obtained by artificial (e.g. solid-phase) synthesis.

As used herein, the term “different amino acid residue” refers to a known amino acid residue other than cysteine unless otherwise indicated. For example, said amino acid residue may be a naturally occurring amino acid residue, such as serine or isoleucine.

As used herein, the term “linear form” refers to proteins according to the present invention that lack secondary structure. Such proteins are often assumed to exhibit a random-coil conformation in which the only fixed relationship is the joining of adjacent amino acid residues by a peptide bond.

In a preferred embodiment, the (isolated) recombinant protein as herein disclosed and claimed is present in monomeric form and/or linear form.

As used herein, the term “treatment” refers to the administration of the (isolated) recombinant protein, as disclosed and claimed herein, and/or the corresponding vaccines and/or immunogenic compositions and/or pharmaceutical compositions in order to obtain the desired clinical results including prophylactic and/or therapeutic treatment.

As used herein, the term “immunotherapy” refers to a therapeutic and/or prophylactic treatment of a subject, e.g. by prophylactic and/or therapeutic vaccination.

As used herein, the term “vector” in connection with “transmission of one or more infectious disease(s)” refers to an alive organism and is herein interchangeably used with terms “biological vector”, “biological carrier” and/or “disease carrier”, such as blood feeding flies, midges, ticks and/or mosquitos.

Furthermore, it is possible, and preferred, that the (isolated) recombinant protein, as disclosed and claimed herein, contains in addition at least one tag module. That is, it is possible, and preferred, that one or more different and/or identical tag modules are part of the (isolated) recombinant protein, as disclosed and claimed herein. Tag modules may be short peptides, frequently consisting of up to 20 amino acids or functional groups which are not composed of amino acids, such as for example biotin or digoxigenin. Suitable tag modules include the well-known and preferred His-tag containing a histidine sequence of 4 to 12 or more, preferably directly consecutive histidine residues, preferably 5, 6 or 7 consecutive histidine residues. Other suitable tag modules include HA-tag, FLAG-tag, GST-tag or Strep-tag. Although the tag can be present anywhere in the (isolated) recombinant protein, as disclosed and claimed herein, in a preferred embodiment, the tag module is present at the N-terminus and/or at the C-terminus of the (isolated) recombinant protein.

The tag modules are useful for isolating the (isolated) recombinant proteins, as disclosed and claimed herein, and in addition allow detecting the presence of such (isolated) recombinant proteins in vitro or in vivo. Furthermore, the tag module optionally together with one or more adjacent amino acid residues from an adjacent module or a linker spacing apart the different modules can be used in order to induce a specific immunologically detectable signal, (e.g. an antibody) in the target subject that can be used as a surrogate marker for immunity and/or duration of immunity. Immunotherapies with the (isolated) recombinant proteins, as disclosed and claimed herein, elicit an antigen-specific, preferably allergen-specific immune response in the target subjects that is qualitatively indistinguishable from the natural immune response after exposure to naturally existing antigens, preferably allergens. Thus, antibodies binding to the antigen module are not suitable for the purpose of being a surrogate marker for the efficiency of the iMAT induced immune modulatory effect. This obstacle can be eliminated by determining the unique, antigen-specific immunological signal obtained by the C-terminal and/or N-terminal tag module—optionally together with the adjacent amino acid residues. Hence, it is possible to provide suitable surrogate markers accordingly.

In a preferred embodiment, the (isolated) recombinant protein, as disclosed and claimed herein, further comprises at least one tag module, preferably at least one His-tag, wherein such at least one tag module preferably is present N-terminally and/or C-terminally of the (isolated) recombinant protein, more preferably N-terminally after one methionine residue.

Moreover, the modules of the (isolated) recombinant protein, as disclosed and claimed herein, namely, the at least one translocation module, the at least one targeting module and the at least one antigen module may optionally be spaced apart by one or more spacer modules located between at least two of such modules.

The spacer modules may be, in particular, peptide sequences or organic molecules. Numerous spacer molecules which can be used for the purposes of the invention are known in the art. In addition, it is also possible to use spacer molecules which will be developed or discovered in future for the purposes of the invention. Suitable spacer modules are, inter alia, peptide spacers, crosslinkers, natural or synthetic polymers such as, for example, nucleic acids, substituted or unsubstituted hydrocarbons, etc.

The coupling can take place both by covalent (preferred) and by non-covalent linkages. The spacer modules have the task inter alia, of separating the various modules of the (isolated) recombinant protein, as disclosed and claimed herein, from each other in space so that they do not have adverse effects on each other with regard to their functionality. Modules of the (isolated) recombinant protein for the purposes of the invention can be coupled by one or more spacer modules which can be cleaved by chemical and/or enzymatic reactions, e.g., by proteases. It is thus possible to separate the modules of the (isolated) recombinant protein, as disclosed and claimed herein, which are connected by the spacer modules, from each other as required.

In a preferred embodiment, however, in particular if the antigen module is an amino acid sequence derived from at least one full or partial epitope of at least one antigen being at least one allergen, no any such additional spacer modules, i.e., no additional spacer modules between two or more adjacent modules of such first, second and/or third modules at all are present.

Any desired arrangement of the individual modules of the (isolated) recombinant protein, as disclosed and claimed herein, is in general possible. Each module may be present one or more times in the (isolated) recombinant protein. The minimum requirement is the presence of at least one translocation module, at least one targeting module and at least one antigen module. Additional modules, such as tag modules, spacer modules, etc. may optionally be present but do not need to be present. All modules may be present one or more times in the (isolated) recombinant protein, as disclosed and claimed herein. If modules are present more than once, they may be present in the form of identical copies, or different versions of a module may be present in each case in a single copy or in more than one copy. It is also possible for entirely different modules of the same class of modules, e.g., a His-tag module and a biotin-tag module, to be present in the (isolated) recombinant protein, as disclosed and claimed herein. Both modules undertake functionally the same task (tag module) in the (isolated) recombinant protein, but do not need to have anything in common in terms of their molecular structure.

In a preferred embodiment, it is possible that two or more copies of one of the modules are present in the (isolated) recombinant protein, as disclosed and claimed herein. That is, two or more copies of identical or different antigen modules may be present. Alternatively, the (isolated) recombinant protein may contain two different antigen modules, for modulating the immune response in a subject.

Two or more identical copies of an antigen module in a recombinant protein may for example cause an enhanced immune response to such relevant antigen. Two or more different antigen modules may for example be combined in one (isolated) recombinant protein in order to modulate simultaneously the immune response towards two or more different antigens. Two or more different translocation modules can be used in the (isolated) recombinant protein, as disclosed and claimed herein. For example, a Tat sequence and a VP22 sequence can serve to make translocation more efficient since the translocation of the (isolated) recombinant protein then takes place efficiently in a broader spectrum of different cell types or tissue types. It is also possible for example to use two or more tag modules in one (isolated) recombinant protein, e.g., a His-tag and a FLAG-tag, in which case for example the His-tag is used to isolate the recombinant protein and for example the FLAG-tag serves to detect the (isolated) recombinant protein. It is possible to use two or more different targeting modules in one (isolated) recombinant protein, e.g., a sequence from the invariant chain of the MHC II molecule and as a further targeting module, a mannose 6-phosphate group. For example, the invariant chain acts as targeting module into the MIICs, and the mannose 6-phosphate group mediates targeting into the lysosome, thus it being possible to increase the efficiency of antigen presentation or the number of different epitopes of the antigen presented by the antigen-presenting cells overall. In addition, the iMAT molecule of the present invention may encompass two or more different invariant chains stemming from identical or different species, thus, allowing using the proteins according to the present invention in different species.

The position of the individual modules within the (isolated) recombinant proteins, as disclosed and claimed herein, can also be varied as desired, as long as at least one translocation module, at least one targeting module and at least one antigen module are present. It is also possible for all or some of the modules of the (isolated) recombinant protein for example to be present not in the form of a linear sequential arrangement of modules, but as circular or as branched module structure or else in the form of dendrimers, or as a combination of linear and/or branched and/or circular and/or dendrimeric molecule portions. There are commercial suppliers of expression vectors which supply specific vectors which make it possible to prepare circular fusion proteins by these mechanisms, such as, for example, the IMPACT™-TWIN system from New England Biolabs, Beverly, Mass., USA. Branched modules might be prepared for example by synthesizing peptides in which, starting from poly L-lysine, a new lysine residue is attached to both free amino groups of each of the subsequent lysine residues. In this way it is possible to create a peptide structure with virtually any extent of branching. It is then possible to synthesize, for example, translocation modules and/or targeting modules subsequently onto the branched peptide basic structure. Further modules can also be coupled onto a linear, circular or branched peptide basic structure by protein ligation. It is also possible to introduce for example biotin groups into the peptide basic structure during the peptide synthesis, and modules can then be attached to these biotin groups via, for example, streptavidin, the Strep tag system or via the PINPOINT™ system (respectively IBA GmbH, Göttingen, Germany and Promega Biosciences Inc., San Louis Obispo, Calif., USA). Modules attached in this way are then coupled via non-covalent linkages to the peptide's basic structure.

In a preferred embodiment, the (isolated) recombinant protein, as disclosed and claimed herein, comprises, preferably consists of one or more of the amino acid sequences according to SEQ ID NOS: 7, 8, 9, 10, 11, 12, 13, 14, 17, 20, 21, 22, 23.

The (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in equines suffering from insects bite hypersensitivity (IBH) and/or urticaria.

Insect bite hypersensitivity may be induced by otherwise harmless insect saliva, venom, body parts, excretions or secretions causing systemic responses in subjects. Actually, IBH is a distressing common allergic skin disease of equines and manifest as a chronic relapsing seasonal allergic dermatitis often caused by the bites of insects of the genus culicoides found in various areas of the world. IBH has been reported worldwide with different names such as sweet itch, summer itch, summer eczema, Kasen, Queensland itch, seasonal dermatitis or Culicoides hypersensitivity. Affected subjects are very itchy and distressed, and rub and bite themselves intensively. A typical clinical sign is pruritus, the fly bites form blisters, which can weep, causing crusting, scabs and scaling. Prolonged rubbing and biting results in, among others, hair loss and damage to the skin, with sometimes bleeding open sores. Occasionally, secondary bacterial infections can occur. It is also not uncommon for horses to rub off their mane and upper tail hair. In the long term, skin thickening and loss of hair pigmentation may occur. The mane and tail are most commonly affected; however, horses with severe signs may have lesions on large areas of the entire body. A diagnosis is based on clinical examination and typical, seasonally occurring signs.

Little is known of the pathophysiology of IBH in horses. There seems to be considerable differences to allergies with manifestation in the skin as compared to other species. Thus, also their response to treatment differs—e.g., histamine receptor antagonists are not able to ameliorate the clinical symptoms (Olsen et al. Vet. J. 2011, 187: 347-351). Also allergen-specific immunotherapy (SIT) has been employed with no success in the past in IBH in horses (Ginel et al., Vet. Derm. 2014, 25: 29-e10).

In order to solve this medical problem the at least one antigen module in an IBH dedicated (isolated) recombinant protein, as disclosed and claimed herein, is selected from a group of recently discovered allergens isolated from midges of different species of the genus Culicoides (Diptera: Ceratopogonidae).

Additionally, IBH-affected horses have a 7.1-times increased risk of also suffering from urticaria [Kehrli D et al, J Vet Intern Med 2015, 29(1): 320-326]. Urticaria, also known as ‘hives’ or as ‘nettle rash’ is characterized by discrete swellings appearing in the skin. These may be circular patches, ring-shaped lesions, mimic a horseshoe shape or have other unusual shapes. The majority of cases are recurrent, of sudden onset of urticaria and do spontaneously resolve within 24-48 hours or several days.

There is good evidence that there are IgE mediated allergic components involved in urticaria. However, the pathophysiology is still poorly understood. Immediate triggers can be insect stings or bites, dietary, drug reaction, bedding, chemicals, etc., in a predisposed subject, e.g., horses suffering from IBH and/or that are otherwise predisposed for a dermal hypersensitivity to environmental allergens. Thus, successful immunotherapy e.g., against IBH may reduce the occurrence of recurrent urticaria in such subjects.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in equines suffering from recurrent airway obstruction (RAO).

Recurrent airway obstruction (RAO) in equines, a respiratory disease similar to human asthma, is one of the most commonly diagnosed conditions affecting the lung of middle aged and older horses all around the world. It is also called heaves, or chronic bronchitis/bronchiolitis, or in earlier days, chronic obstructive pulmonary disease (COPD). When present during summer, e.g., when horses are on pasture, the terms “summer pasture associated obstructive pulmonary disease” or “summer pasture associated RAO” are used.

RAO is a type-1 immediate hypersensitivity allergic disease involving the typical series of events that begin with reaginic antibodies, mainly IgE resulting in mast cell degranulation leading to the production of histamine and other chemical mediators that act together to induce airway inflammation and reversible airway obstruction. The clinical signs observed during exacerbation can be severe and include exercise intolerance, cough, nasal discharge and increased respiratory effort at rest. Diagnostic procedures such as lung function measurement, analysis of blood gas or bronchoalveolar lavage can provide additional information on the disease. Typical treatment involves palliative treatment only (e.g., bronchodilators and/or corticosteroids), but currently no causative treatment is available (Leclere et al. Respirology 2011, 16: 1027-1046, Pirie, Equine Vet J 2014, 46: 276-288).

Recently treatment with a Clara Cell 10 kDa protein (CC10) has been claimed to be effective in protecting or be useful as a passive immunotherapy in horses suffering from RAO. CC10 is one of the members of a family of anti-inflammatory defense proteins produced predominantly in the airway epithelium of man and animals. The invention is described in US 2014/0105906.

RAO is a complex disease, but clearly exposure to airborne allergens plays a pivotal role in the etiology. Clinical remission is usually achieved by eliminating the exposure to the aeroallergens. Though, the major antigens involved in triggering RAO have not been clearly identified so far. Numerous potential agents are present in e.g., organic dust—be it in stabled horses mainly as stable or hay dust or in pastured horses additionally involving pollen (Leclere et al. Respirology 2011, 16: 1027-1046, Pirie, Equine Vet J 2014, 46: 276-288).

The antigen module of iMAT molecules according to the present invention can be selected by a bioinformatics approach as described exemplarily and in detail in Examples 6 and 7 herein. By this means iMAT molecules can be rendered useful specifically as vaccines, e.g., for therapy and/or prevention of RAO in subjects, preferably equines.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in equines suffering from infectious diseases caused by bacteria.

Rhodococcus equi is a soil-dwelling pathogenic actinomycete that causes pulmonary and extrapulmonary pyogranulomatous infections—equine rhodococcosis. Young foals are particularly susceptible and may develop a life-threatening pneumonic disease. Though, ulcerative enterocolitis, osteomyelitis and septic arthritis are occasionally observed. Many immunization strategies have been tried to prevent rhodococcosis in foals, with no to limited success. Antibiotic treatment is inconsistently effective as well as expensive, and recent studies have highlighted the emergence of antibiotics-resistant strains.

The infection is primarily through inhalation of airborne dust carrying the pathogen. On entry into a host, R. equi is taken up by local macrophages, particularly alveolar macrophages in the lung after inhalation. It spreads with slow progressive loss of functional lung, making early clinical diagnosis difficult. Early clinical signs often only consist of a mild fever, occasional cough, or a slight increase in respiratory rate that may not be apparent unless foals are exercised or stressed by handling. Additionally the diagnosis is not that easy—currently a recommended tool for monitoring farms with endemic R. equi pneumonia is the analysis of white blood cell concentrations and the cultivation of bacteria from transtracheal washes and identification of R. equi via PCR or cytological examinations from such material (van Bargen, K and Haas, A. FEMS Microbiol Rev 2009, 33: 870-891, Vazquez-Boland, J A et al., Vet Microbiol 2013, 167: 9-33).

In order to solve this medical problem the at least one antigen module in an rhodococcosis dedicated (isolated) recombinant protein, as disclosed and claimed herein, may be selected from antigens derived from R. equi, e.g., the virulence-associated protein A (VapA), an immunodominant surface-expressed lipoprotein, or other surface proteins, it may also be derived from R. equi-infecting phages. Improved MAT molecules may be achieved useful specifically as vaccines, e.g., for therapy and/or prevention of equine rhodococcosis. The treatment may involve the administration of the iMAT molecule to the foal and/or may also comprise a treatment of the pregnant mare according to the present invention.

Strangles is another example of infection in horses, Strangles, characterized by abscessation of the lymph nodes of the head and neck, is caused by Streptococcus equi and is one of the most frequently diagnosed infectious diseases of horses and there remains a significant need to develop new preventative vaccines.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in equines suffering from infectious diseases caused by viruses.

African horse sickness (AHS) is a highly infectious and deadly disease. It commonly affects horses, mules, and donkeys. It is caused by a virus of the genus Orbivirus belonging to the family Reoviridae. AHS is not directly contagious, but is known to be spread by insect vectors, mainly by Culicoides, but also Culex, Anopheles and Aedes, or transmission by ticks (e.g., Hyalomma or Rhipicephalus) has been described. To date no effective treatment exists for AHS and close to 90% of the infected horses die mostly due to respiratory failure with 24 h of the infection. Consequently, control of the disease relies on preventive vaccination.

West Nile virus (WNV) is a mosquito-transmitted positive-stranded RNA virus grouped within the Japanese encephalitis virus serocomplex of the genus Flavivirus in the family Flaviviridae. The WNV is the causative agent of the disease syndrome also named West Nile Fever. Birds are the natural reservoir hosts, and WNV is maintained in nature in a mosquito—bird-mosquito transmission cycle. However, when horses are infected it remains frequently unrecognized. Horses have died or are euthanatized because of severe neurologic signs—including paresis, ataxia, recumbency, and muscle fasciculation; others exhibit mild to severe polioencephalomyelitis. Diagnosis and confirmation of WNV infection can be made directly by identification of the virus or indirectly by testing for antibodies in clinical specimens. It is, however, hampered by typically short duration and low level of the viraemia in horses.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the prevention of transmission of infectious diseases in equines by vectors, e.g., blood feeding flies, midges, ticks and/or mosquitos.

The pathogens are delivered into the skin of the mammalian host along with arthropod saliva, which contains a wide variety of bioactive molecules. These saliva components are capable of altering hemostasis and immune responses, and may contribute to the ability of the pathogen to establish an infection. The presence of infectious microorganisms in the salivary glands of blood-feeding arthropods itself alters saliva composition, such as changes in the concentration of apyrase or anti-thrombinase in infected mosquitoes. These antigens or others are well suited to be employed in the antigen module of iMAT molecules according to the present invention and may be useful specifically as vaccines to activate the host immune system to prevent the transmission of infectious pathogens by vectors in equines.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in equines suffering from infectious diseases caused by fungi.

Dermatophytosis or ringworm is a fungal infection of the hair and of the superficial keratinized cell layers of the skin occurring in animals and man. Several species of genus Microsporum or genus Trichophyton belonging to the groups of zoophilic or geophilic dermatophytes can cause clinical infections in animals. A variety of surface antigens of the fungi and/or their spores are well suited to be employed in the antigen module of iMAT molecules according to the present invention, and may be useful specifically as vaccines, e.g., for therapy and/or prevention of dermatophytosis in equines.

In a further embodiment the (isolated) recombinant proteins, as disclosed and claimed herein, are in particular useful in a method for specifically addressing the therapy and/or prophylaxis in equines suffering from infectious diseases caused by parasites.

Parasites infecting horses are ubiquitous and clinically important across the world. The major parasitic threats to equine health are cyathostomins, parascaris equorum, anoplocephala perfoliata, and strongylus vulgaris. Increasing levels of anthelmintic resistance is reported worldwide in equine parasites. For protozoa, e.g., cryptosporidium few drugs consistently inhibit parasite reproduction in the host. Mainly foals are affected and outcome relies on innate and adaptive immune responses.

Antigens deriving from adult parasites as well as prepatent stages are another example to be employed in the antigen module of iMAT molecules according to the present invention and may be useful specifically as vaccines, e.g., for therapy and/or prevention of parasite infection in equines.

In particular in case of modulating the immune response in horses, the at least one targeting module preferably is the equine invariant chain, more preferably one or more amino acid sequences according to SEQ ID NOS: 2, 15, 16.

In an advantageous embodiment, the (isolated) recombinant protein, as disclosed and claimed herein, is present in a monomeric form since, for instance, recombinantly introduced allergens tend to aggregate formation, particularly, if produced via inclusion bodies. By substituting at least one, and more preferably all cysteine residues in the entire sequence of the (isolated) recombinant protein, preferably by substituting for serine, leucine, isoleucine and/or aspartic acid, it is possible to prevent intermolecular disulfide bond formation, thus, avoiding any aggregation, in particular, any non-native formation of inter- and/or intramolecular bonds. That is, the (isolated) recombinant protein being entire devoid of cysteine residues does not aggregate. Consequently, the protein is easily expressible and demonstrates improved targeting and MHC presentation.

Furthermore such cysteine-free variants of, for instance, allergens, in which the cysteine residues in the amino acid sequence of wild-type allergens have been mutated singly or in combinations, show a reduced IgE reactivity compared to the corresponding wild-type allergens and at the same time have substantially retained reactivity towards T-lymphocytes and are thus hypoallergenic.

The invention accordingly relates to such hypoallergenic variants of allergens eliciting for example IBH in horses, wherein in the variants the cysteine residues of wild-type allergens have been mutated singly or in combinations.

Furthermore, the presence of a tag module for separating proteins in a sample, comprising the iMAT molecules according to the present invention, e.g. using zinc- or cobalt-charged solid support further improve the possibility to produce fusion proteins without aggregates during the purification process. Typically, the tag module includes a polyhistidine tag of five to six consecutive histidine residues.

The (isolated) recombinant proteins, as disclosed and claimed herein, are useful in a pharmaceutical composition. For example, the (isolated) recombinant proteins are for use in a vaccine. Hence, the present invention provides vaccine compositions containing one or more (isolated) recombinant proteins, as disclosed and claimed herein. Such vaccine composition can be used therapeutically and/or prophylactically in equines suffering from insect bite hypersensitivity (IBH), urticaria and/or equine recurrent airways obstruction (RAO), infectious diseases induced by pathogens, e.g. rhodoccus pneumonia, strangles, African horse sickness, West Nile Virus infection, dermatophytosis and/or parasites of the digestive tract or other organs, e.g., cryptosporidiosis, helminths and/or their prepatent stages. Additionally, the method can be used not only directed against such pathogens, but also to activate the host immune system to prevent the transmission by vectors, e.g., blood feeding flies, midges, ticks and/or mosquitos.

Thus, in a preferred embodiment of the present invention a vaccine for subjects, such as equines, is provided in order to treat and/or prevent IBH caused by a response to the bites of e.g. Culicoides midges and/or other blood feeding insects. Additionally, successful immunotherapy against IBH may reduce generally the dermal hypersensitivity to environmental allergens and thus may reduce the occurrence of recurrent urticaria in such predisposed subjects.

In a further embodiment of the present invention a vaccine for subjects, such as equines, is provided in order to treat and/or prevent RAO caused by a response to e.g., mold (fungi and/or their spores), pollen, house dust or forage mites (and/or their feces).

In a further embodiment of the present invention a vaccine for subjects, such as equines, is provided in order to treat and/or prevent infectious diseases involving e.g. the genera rhodococcus, streptococcus, orbivirus, flavivirus, trichophyton, microsporum, cryptosporidium and/or strongylus. Additionally, the vaccine can be provided to activate the host immune system to prevent the transmission of a disease by vectors, e.g., culicoides, culex and/or ixodes and/or other blood feeding insects.

The pharmaceutical composition, e.g., in form of a vaccine, of the (isolated) recombinant proteins is preferably designed for sublingual administration, subcutaneous and/or intradermal injection, injection into a lymph node and/or for administration via the mucous membranes, in particular, via the mucous membranes of the gastrointestinal tract or of the respiratory system.

In a preferred embodiment of the present invention, the pharmaceutical compositions are administered parenterally.

The iMAT molecules according to the present invention can be used as a pharmaceutical or as a vaccine to modify, for instance, allergic disorders. For example, insect bite hypersensitivity (IBH) can be treated by such iMAT molecules.

Low amounts (1 to 1000 μg referring to the weight of solely the one or more antigen modules) of the recombinantly produced iMAT molecules comprising allergens of IBH eliciting insects as of the genus Culicoides e.g., injected 1 to 5 times subcutaneously, intradermally or directly into the lymph node, induce a strong and long lasting immune response in horses leading to an amelioration of clinical symptoms.

In one preferred embodiment, the iMAT molecules of the present invention are administered in combination with at least one adjuvant. The adjuvant includes, but is not limited to, one or more of the following: alum, BCG, aluminium hydroxide, aluminium phosphate, calcium phosphate, lipid emulsions, lipid or polymeric nano- or microspheres, micelles, liposomes, saponin, lipid A, or muramyl dipeptide, bacterial products, chemokines, cytokines and hormones, chitosan, starch, alginate, cellulose derivatives (e.g., ethyl cellulose, hydroxypropylmethyl cellulose), nucleic acids, or a nucleic acid construct. One or more of these components may be added to enhance or modify the immune response. Alternatively, the iMAT molecule may be administered without an adjuvant or in an aqueous form.

The iMAT molecules may be administered in a dose of about 1 μg to 1000 μg (this and the subsequent doses referring to the weight of solely the one or more antigen modules) and more preferably in a dose from about 10 μg to about 100 μg and even more preferably in a dose from about 20 μg to about 50 μg, although the optimal dose may vary depending on the antigen, preferably allergen, being injected, the weight of the subject, the immune system of the subject, and alike. Effective treatment in many cases may be accomplished with one administration. In some embodiments, treatment includes from 1 to 15 administrations. In preferred embodiments, treatment includes from 1 to 5 administrations and more preferably 1 to 3 administrations. For initial treatment administrations may be periodically, e.g., over a course of days, once or twice per month or year, or several times a year. For maintenance of immune response, administrations may be done in intervals of several months to several years.

In a preferred embodiment of the present invention, the (isolated) recombinant proteins, as disclosed and claimed herein, are designed for lymphatic intranodal administration. In the course of direct injection into a lymph node, the respective lymph node may be visualized during the injection procedure e.g., by ultrasound, in order to monitor the location of the needle and changes in the lymph node, such as swelling. Injection into the mandibular, axillary, inguinal and/or popliteus lymph nodes is preferred due to ease of ultrasound guided location and injection.

It is known in the art that several (>20) of the identified proteins in saliva of blood feeding insects induce IgE reactivity and pathological dermal reactions in horses [Schaffartzik, Veterinary Immunology and Immunopathology 2012, 147: 113-126; Allergome (allergome. org)]. Thus, it is expected that a treatment can only be successful, if most of the relevant allergens are included in a medicament for specific immunotherapy. However, surprisingly only 1, 2, 3 or 4 of such iMAT molecules according to the present invention each comprising different antigen modules e.g., of insect saliva or a mosaic-like construct of only epitopes are sufficient to induce an immunomodulation and/or clinical improvement of the diseased subjects if such iMAT molecules are injected 1 to 5 times subcutaneously, intradermally and/or directly into the lymph node.

In a preferred embodiment, a single iMAT molecule is employed and is sufficient for the induction of a therapeutic effect and/or prevention of development of insect bite hypersensitivity (IBH), urticaria and/or equine recurrent airways obstruction (RAO) in equines.

In another preferred embodiment, a combination of 2, 3 or 4 iMAT molecules is employed by means of simultaneous, sequential and/or a chronologically staggered co-administrations.

In a preferred embodiment, a single iMAT molecule is employed and is sufficient for the induction of a therapeutic effect and/or prevention and/or prevention of transmission of infectious diseases in equines e.g., rhodoccus pneumonia, strangles, African horse sickness, West Nile Virus infection, dermatophytosis and/or parasites of the digestive tract or other organs, e.g., cryptosporidiosis, helminths and/or their prepatent stages and/or the transmission of such infectious diseases by e.g., blood feeding flies, midges, ticks and/or mosquitos.

In another preferred embodiment, a combination of 2, 3 or 4 iMAT molecules is employed by means of simultaneous, sequential and/or a chronologically staggered co-administrations.

Depending on the thermodynamic evaluation of the (isolated) recombinant protein, as herein disclosed and claimed, stability is influenced by the cysteine mutation, namely the substituting different amino acid residue(s). For example, the substitution may be a Cys to Ser substitution. However, the stability may be higher using a different amino acid residue than the Ser amino acid to achieve the desired stability and solubility. That is, while a first choice may be substitution of Cys with Ser, in case of instability, other amino acid residues than Ser should replace Cys.

In order to select stabilizing amino acid residues as replacements for cysteine residues in targeted sequences a three step approach is chosen:

-   -   1. Modeling the tertiary structure of the targeted protein         including terminal hexahistidine tags, iMAT sequence and the         primary amino acid sequence of the protein of interest. Modeling         can be conducted with the native sequence and with cysteine         substitutions.     -   2. Iterative determination of protein stabilities based on         single point substitutions, such as substitution of a cysteine         residue with a different amino acid residue, e.g., Ser and/or         Ile, and scoring to determine stabilizing replacements by         analyzing all available three dimensional structures.     -   3. Re-Modeling of the stabilized structure and validation of the         stability by repeating step 1 and 2.

Three-dimensional protein structures are crucial for understanding protein function on a molecular level and are of great interest for the rational design of many different types of biological experiments, such as site-directed mutagenesis. However, the number of structurally characterized proteins is small compared to the number of known protein sequences. It is possible to identify a homologous protein with a known structure (template) for a given protein sequence (target). In these cases, homology modeling has proven to be the method of choice to generate a reliable 3D model of a protein from its primary amino acid sequence. Building a homology model comprises four main steps: (1) identification of structural template(s), (2) alignment of target sequence and template structure(s), (3) model building and (4) model quality evaluation. These steps can be repeated until a satisfying modeling result is achieved. In cases where no accurate homologue model can be determined, computational approaches to determine a protein structure from the primary structure (amino acid sequences) are used. “De novo” or “ab initio” methods are based on physical principles and try to imitate the folding process. Such methods have to sample a large number of conformations and require very accurate energy functions to identify structures in the global minima of free energy. Many methods use a combination of these described principles.

The availability of computational tools yielding reasonably accurate estimations of the impact of amino acid substitutions on the stability of proteins is of crucial importance in a wide range of applications. In particular, such tools have the potential of stimulating and supporting protein engineering and design projects dedicated to the creation of modified proteins.

Protein stability can be regarded in terms of the thermodynamic stability of a protein that unfolds and refolds rapidly, reversibly. In these cases, the stability of the protein is the difference in Gibbs free energy between the folded and the unfolded states. The only factors affecting stability are the relative free energies of the folded and the unfolded states. The larger and more positive the folding free energy difference is, the more stable the protein is to denaturation. The folding free energy difference is typically small, of the order of 5-15 kcal/mol for a globular protein. However, on the other hand, protein stability can be regarded as a protein property to withstand harsh temperature or solvent conditions. This is related to the thermodynamic stability but also to reversibility or irreversibly of folding/unfolding (kinetic stability).

To predict the thermodynamic stability changes caused by single site substitutions in proteins, several different approaches can be applied to study the impacts of such substitutions on protein structure and function [Pires D E et al., Bioinformatics 2014, 30(3):335-342]. Such approaches can be broadly classified into those that seek to understand the effects of substitutions from the amino acid sequence of a protein alone, and those that exploit the extensive structural information. Structure-based approaches typically attempt to predict either the direction of change in protein stability on substitutions or the actual free energy value (ΔΔG).

The results for each specific protein and its corresponding models are statistically analyzed in terms of the number of appearances of specific substitutions using a scoring system, that grades the replacement based on occurrences in used models and the protein stability free energy change (ΔΔG) thereby determining most destabilizing residues (if any) within the input structure and possible replacements. The score is calculated by determination of the lowest ΔΔG (ΔΔG<0) at each position of interest in each model and assigning corresponding linear values and cumulative ΔΔG's values for each potential replacement position and results are than evaluated to determine consistency among models. Since calculated protein models possess different qualities (the probability of predicting the correct three-dimensional structure) a weighting factor can be implemented to prioritize results from more accurate models. A significant (based on the ΔΔG) destabilizing residue (if any) is substituted; new models are generated and re-analyzed iteratively until a steady state is reached. Additionally generated models are evaluated by analyzing the xyz coordinates via principal component analysis to determine potential structural misfoldings due to replacement of amino acids at specific positions.

In yet a further aspect, the objective underlying the invention has surprisingly been solved by providing a method of identifying amino acid substitutions in a predetermined amino acid sequence allowing the stabilization of such predetermined amino acid sequence comprising the steps of:

-   -   i. modeling of the three-dimensional/tertiary structure of the         targeted predetermined amino acid sequence,     -   ii. iterative determination of protein stabilities based on         single point substitutions, such as substitutions of cysteine         residues with different amino acid residues, preferably serine         and/or isoleucine residues, and a scoring system based on the         protein stability free energy changes (ΔΔG) to determine         stabilizing substitutions by analyzing all available         three-dimensional/tertiary amino acid sequence structures,     -   iii. re-modeling of the substituted three-dimensional/tertiary         amino acid sequence structure and calculation of its stability         by repeating steps (ii) and (iii) until a steady state is         reached;

In yet a further aspect, the objective underlying the invention has surprisingly been solved by providing an (isolated) recombinant protein as herein disclosed and claimed, wherein its full or partial amino acid sequence was stabilized by the method of identifying amino acid substitutions in a predetermined amino acid sequence as herein disclosed and claimed (see Example 5 herein).

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: shows examples of allergens of the genus culicoides identifying the species, the allergen and the uniprot accession number (database release is UniProt release 2013_09)

FIGS. 2A and 2B show an SDS-PAGE of MAT-Fel d1 (IVN201) under reducing conditions; FIG. 2A) Original SDS-PAGE (10 μg protein per lane, Coomassie staining) and FIG. 2B) SDS-PAGE with bands that have been cut out of gel A and reloaded on SDS-PAGE (silver staining)

FIG. 3: shows an SDS-PAGE of Fel d1 under reducing conditions; NUPAGE® 4-12% Bis-Tris Gel. Lanes: 1) Marker: SeeBlue Plus2 Pre-Stained Standard 2) 5 μg Fel d1; 3) 5 μg Fel d1

FIG. 4: shows an RP-HPLC chromatogram 0.1% TFA/Acetonitril gradient a) native protein (MAT-Fel d1) without additives (left graph); b) MAT-Fel d1 denaturated by addition of guanidinium chloride plus DTT (right graph)

FIG. 5: depicts MAT-Fel d1 molecule and its Kyte-Doolittle hydrophobicity plot

FIG. 6: shows a NUPAGE® SDS-PAGE-System (4-12% Bis-Tris Gels, 1×MES-Running buffer, 35 min, 200 V). Lanes: 1) Lysozyme, 1 μg Protein ox. 2) PageRuler Prestained Protein Ladder; 3) MAT-Fel d1 (5 μg) oxidized with lodacetamide (ox.); 4) iMAT-Cul o4 (ox.); 5) PageRuler Prestained Protein Ladder; 6) MAT-Fel d1 (5 μg) reduced; 7) iMAT-Cul o4 reduced; 8) Lysozyme reduced

FIG. 7: shows an RP-HPLC chromatogram 0.1% TFA/Acetonitril gradient. The peak reflects native (oxidized) protein (iMAT-Cul o4) without additives

FIG. 8: depicts an example of display of counts of local alignments hits of selected Culicoides allergens in comparison to sensitizations measured (see description for details). The figure depicts the comparison between the antigenic prediction (light gray and right Y-axis) and the outcome (dark gray and left Y-axis) in a HRT test in terms of severity (total score values per allergen) in a cohort of IBH horses. The severity describes the degree of a reaction in the test in a semi-quantitative scale (left Y axis). The data from the prediction is scaled by setting the highest occurrence score equal to the highest severity score.

FIG. 9: shows the results of the following experiment: Proteins and ADJU-PHOS® that were incubated at RT for 30 min while mixing gently. After incubation, the samples were centrifuged for 3 min. and subsequently analyzed by SDS-Page Lane 1) pageRuler Prestained Protein Ladder; 2) iMAT-Cul o3 Supernatant; 3) iMAT-Cul o3 Pellet in Urea 4) iMAT-Cul o3 Supernatant; 5) iMAT-Cul o3 Pellet in Urea; 6) Empty; 7) iMAT-Cul o2 Supernatant 8) iMAT-Cul o2 Pellet in Urea 9) iMAT-Cul o2 Supernatant 10) iMAT-Cul o2 Pellet in Urea; 11) Empty; 12) iMAT-Cul o4 Supernatant; 13) iMAT-Cul o4 Pellet in Urea 14) iMAT-Cul o4 Supernatant; 15) iMAT-Cul o4 Pellet in Urea; (2, 3, 7, 8, 12, 13 w/o freeze thaw); (4, 5, 9, 10, 14, 15 after two times freeze thaw process)

FIG. 10: shows Histamine Release Test (Details of assay in Example 2) of 5 concentrations of iMAT-Cul o2 and iMAT-Cul o3 and the respective allergens in a polysensitized horse (Horse 1)

FIG. 11: shows the Kyte-Doolittle hydrophobicity plot of MAT molecules versus iMAT molecules in the generic part of the respective fusion proteins [i.e. without the respective antigen module(s)]. The hydrophobicity index is shown on the Y-axis versus the amino acid position on the X-axis. Positive numbers in the index indicate hydrophobicity. The shift of the graph of the iMAT molecule at the beginning of the hydrophobicity plot as compared to the MAT molecule is due to the additional N-terminal presence of a His-tag and one methionine residue in the iMAT molecule as well as the absence of any spacer module(s).

FIG. 12: shows the number of non-random hits for each peptide with a length of 13 amino acids for Cul o3 (M4X062, SEQ ID NO: 6) in the canonical database and their position within the corresponding precursor protein. The y-axis depicts the number of hits and the x-axis the amino acid position in reference to the precursor protein. Vertical dotted lines indicate cysteine residues, the dotted-dashed line depicts the moving average of the number of non-random found homologies and horizontal solid lines correspond to in silico cleaved peptides.

EXAMPLES

The following examples serve to further illustrate the present invention; but the same should not be construed as a limitation of the scope of the invention disclosed herein.

Example 1—Surrogate Marker for Immunity/Duration of Immunity

Administration of an (isolated) recombinant protein, as disclosed and claimed herein, to an equine produces an immunological response to the allergen and/or epitope present in the antigen module. Additionally, the C- or N-terminal tag module together with the adjacent amino acid residues from the adjacent module can be used in order to detect a unique product-specific immunological signal (e.g. an antibody—or a T-cell response) in a target subject that can be used as a surrogate marker for immunity or duration of immunity. This surrogate marker, as a treatment-specific immunological parameter, enables the assessment of immunity or immune modulation or the duration of immunity or the duration of immune modulation after the administration. Thus, a specific indicator for an immune response triggered by the (isolated) recombinant protein according to the invention is the induction of terminal-tag (optionally with the adjacent amino acid residues) specific antibodies, such as IgG antibodies. Alternatively or additionally, the indicator is the induction of antibodies specific to the junction of a spacer and a module as described and claimed herein or the junction between two modules.

Example 2—Hypoallergenicity

Freshly withdrawn blood of horses suffering from IBH can be prepared to test the basophil reactivity to (isolated) recombinant proteins/iMAT molecules, as disclosed and claimed herein. This can be determined by a modified method of Kaul [Kaul, S., 1998. Type I allergies in the horse: Basic development of a histamine release test (HRT). Doctoral thesis. Veterinary School Hannover, Germany]. Briefly, a 10-fold dilution series (e.g. ranging from 10 nM to 0.001 nM final allergen concentration) of iMAT molecules and/or recombinant allergens is prepared in PIPES buffer (AppliChem, Darmstadt, Germany), pH 7.4. Washed red and white blood cells obtained from Na-EDTA coagulation-inhibited blood are incubated with individual dilutions for 1 h at 37° C. The reaction is stopped by incubation on ice for 20 min and the supernatant containing the released histamine is collected from each sample after centrifugation. Maximal histamine content is obtained by boiling the blood cells for 10 min in a water bath (maximal release). The incubation of releasing buffer with washed blood cells served as a negative control (spontaneous release). Histamine concentrations are determined using a competitive RIA (LDN Nordhorn, Germany) as per the manufacturer's instructions.

Alternatively, another basophil activation test is the Cellular Antigen Stimulation Test CAST® ELISA which can also be considered as an in vitro allergy provocation test. This assay is done according to the manufacturer's instructions (Bühlmann Laboratories AG, Allschwil, Switzerland). In the CAST®, sedimented leukocytes from allergic subjects' blood are simultaneously primed with the cytokine IL-3 and stimulated with iMAT molecules and/or recombinant allergens. Basophilic cells among others generate the allergic mediator, sulfidoleukotriene LTC4, and its metabolites LTD4 and LTE4. These freshly synthesized sulfidoleukotrienes (sLT) are subsequently measured in an ELISA test (Enzyme Linked Immunosorbent Assay).

The potential of iMAT molecules to induce adverse events, e.g., provoke anaphylaxis as a side effect of administration can be evaluated in vitro with these assays by comparing the effects of the iMAT molecules (containing an allergen) to the respective recombinant allergen alone.

A reduced basophil degranulation, e.g., histamine and/or sulfidoleukotriene release by iMAT molecules as compared to the recombinant allergen indicates a lower potential for adverse effects, i.e., a better safety profile of the iMAT molecules.

Said HRT (or CAST®) can be used as an in vitro provocation test for type 1 allergic reactions in horses. Allergen specific histamine release indicates the relevance of the respective allergen for the basophilic cell activation and thus can be used as a quantitative parameter for the allergen specific sensitization of a subject.

With MAT molecules described in the prior art, hypoallergenicity could be demonstrated in comparison to the corresponding native allergen (Fel d1) [Senti G et al., J Allergy Clin Immunol. 2012, 129(5): 1290-1296] in the Cellular Antigen Stimulation Test (CAST®) assay as well as in the intradermal and in the intracutaneous test. The quantitative difference in sensitivity between the allergen and the MAT molecule comprising the Fel d1 was 100-, 23- and 16-fold, respectively. Though MAT-Fel d1 was clearly hypoallergenic, some allergenicity remained.

With regard to the present invention, the safety of 2 iMAT molecules manufactured according to the present invention comprising Cul o2 and Cul o3 in the antigen module, respectively, was tested. Freshly withdrawn blood of a poly-sensitized horse suffering from IBH was employed in the histamine release test (HRT) as described above.

As shown in FIG. 10, the native allergens elicited a strong histamine release whereas surprisingly the two different iMAT molecules (iMAT-Cul o3 and iMAT-Cul o2) showed virtually no response at all.

Thus, iMAT molecules showed clear superiority in respect to safety as compared with the MAT molecule as described in the prior art (see above).

It can be expected that no allergen related adverse reactions occur if horses suffering from IBH are treated with said iMAT molecules.

The consequence of this surprising safety property of iMAT molecules in contrast to MAT molecules is, that iMAT molecules used as desensitizing proteins can be used similar to vaccines against pathogens. No up-dosing as with classical therapeutic allergens is needed, since vaccines comprising iMAT molecules do not show allergen properties with respect to allergic adverse events. Already the dose of the first injection of the iMAT molecule in a treatment course may be selected based on efficacy considerations only, and one does not have to consider potential allergic adverse reactions. This could not be performed using MAT molecules described in the prior art since the allergenicity of MAT, compared to the native allergen, was only reduced to a certain level. However, MAT molecules still are allergens; iMAT molecules, in contrast, are not. The advantage of these improved properties renders a more efficacious treatment regime possible with e.g., three subcutaneous or intralymphatic injections with a high biopharmaceutical content (e.g., 3 times 20 μg to 50 μg iMAT protein).

The lack of allergenicity of the two iMAT molecules tested can be explained by the fact that in contrast to the MAT molecules described in the prior art no linker amino acid residues [i.e. spacer module(s) between the first, second and/or third module(s)] were used to separate the different modules in such iMAT molecules. It is known in the prior art that engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker are important for the function (e.g. epitope recognition by the immune system) of the proteins [Klein J S et al., Protein Eng Des Sel. 2014, 27(10): 325-330]. The separation distance between functional units can impact epitope access and the ability to bind with avidity. If the missing amino acid residue linkers between the modules, in particular between the targeting domain and the antigen module, lead to a more rigid structure, conformational epitopes of the allergen module might not be formed due to incorrect folding. A cross linking of antibodies bound on the surface of basophils (e.g., IgE) by its high affinity receptors is necessary to induce activation and histamine release. However, misfolded allergens might not be able to induce such cross linking. Thus, an iMAT molecule without linker may not form conformational IgE epitopes which renders the iMAT molecules non-allergenic.

Example 3—In Silico Detection of Allergens/Biomarkers

As described in detail in the description of the invention in IBH the major allergens eliciting IBH have not yet been described—the bioinformatical engineering of iMAT antigen modules for targeting IBH may be employed to evaluate in silico the relevance of a certain allergens (see Example 6 herein). For example, as shown in FIG. 8 the in silico as well as the ex vivo functional HRT test results of Cul o3 seem to indicate that Cul o3 is a major allergen. Most of the horses tested, though not all, showed a clear hypersensitivity against Cul o3.

This is surprising, as in other experiments, e.g., by van der Meide et al. (Vet J 2014, 200: 31-37), the different recombinant allergens could not be discriminated in their relevance for the disease: around 80% to 90% of horses suffering from IBH showed a sensitization to each of the allergens tested.

Thus, surprisingly, in the course of the present invention it could be shown that Cul o3 (i) in fact is a major allergen (i.e. >50% of the animals are sensitized) in IBH and (ii) is of superior relevance as compared to other allergens.

Apart from being employed in the iMAT antigen module, the respective allergens can also serve to optimize the treatment success by investigating prior to initiation of the treatment the strength of hypersensitivity against said allergen. And throughout the course of the treatment the allergen specific modulation of the different components of the immune system can be monitored, e.g., changes in allergen specific IgE and IgG antibody titers can indicate therapy and/or prevention effects.

Thus, the in silico detected allergens and/or the respective allergen-specific immunoglobulins may be employed as diagnostic and/or theranostic biomarkers.

Example 4—Therapeutic Vaccine/Prophylaxis of IBH in Equines

A single iMAT molecule or a combination of iMAT molecules containing different antigen modules according to the present invention may be employed for treating prophylactically or therapeutically a horse suffering from or to be at risk of insect bites inducing IBH. In horses, iMAT molecules according to the present invention can be administered into a submandibular lymph node (Landholt et al., Vet Rec 2010, 167: 302-304). Briefly, the hair over the lymph node is clipped and surgically prepared. Using palpation and/or ultrasound for guidance, a 25 G needle is inserted into the lymph node. The injected iMAT molecule is adsorbed to an adjuvant. The adjuvant consists e.g., of aluminum phosphate (ADJU-PHOS®, Brenntag Biosector, Denmark). The iMAT molecule stock is a frozen solution of 375 μg/mL protein concentration in vials, each containing 500 μL to be thawed before use.

After thawing the iMAT molecule solution, 400 μL of the solution are mixed with e.g., 200 μL of the aluminum phosphate gel suspension. This final formulation is left at room temperature for 60 minutes prior to the intralymphatic injection to allow for absorption of the iMAT molecule to the ADJU-PHOS®.e.g., 200 μL of the mixture containing 50 μg iMAT molecule is removed into a 500 μL syringe for lymph node injection. This preparation is first administered typically on day 0, day 28 and day 56 in a dose between 20 μg and 50 μg (referring to the weight of solely the one or more antigen modules) per injection and iMAT molecule.

Throughout the treatment period and/or thereafter the efficacy of a therapy or the prevention of IBH can be investigated clinically by quantitative, semi-quantitative or qualitative assessment of skin lesions (e.g., broken hairs, alopecia, crusts/scrubs and wet areas). The intensity of scrubbing/itching can be scored.

These clinical parameters can be compared to clinical signs of the individual horse in previous IBH seasons and/or to the severity prior to the start of a therapeutic intervention. Alternatively, a comparison to IBH affected horses that are not treated or treated with placebo can demonstrate the efficacy of the iMAT molecule-mediated treatment and/or prevention of clinical signs of IBH.

Fresh blood of said horses can be used in an in vitro provocation test for type 1 allergic reactions in horses, e.g., with HRT or CAST® (for details see Example 3 supra). A reduced basophil degranulation in response to a challenge with certain culicoides allergens, e.g., histamine and/or sulfidoleukotriene release after the iMAT molecule administration, as compared to before, indicate a therapy and/or prevention effect.

Alternatively or in addition an intradermal provocation test [Langner et al., Vet Immunol Immunopathol 2008, 122(1-2):126-37] with certain culicoides allergens can be employed in said horses. A reduced response (immediate and/or late phase reactivity) indicates a therapy and/or prevention effect of the iMAT molecule administration.

Furthermore, the modulation of the different components of the immune system can be monitored, e.g., changes in allergen specific IgE and IgG antibody titers can indicate therapy and/or prevention effects.

Apart from changes in IgE levels, an increase in allergen-specific IgG can be surprisingly found when treating a horse for IBH with such iMAT molecules. These antibodies can block IgE-mediated anaphylaxis in vivo and seem to inhibit not only the allergen-induced release of inflammatory mediators from basophils and mast cells, but also IgE-mediated allergen presentation to T cells. Among the iMAT-induced IgG antibodies specifically binding to the allergen, some allergen-specific subtypes have been suggested to play an important “protective” role, as they compete with allergen-specific IgE antibodies and can prevent the activation of CD4+ T cells, by inhibiting the IgE-mediated antigen presentation. Furthermore, the IgG subset which is secreted promotes a significant reduction in mast cells and eosinophils, accompanied by a diminished release of inflammatory mediators [Senna G et al., Curr Opin Allergy Clin Immunol. 2011, 11(4): 375-380].

The functional assay of serum “blocking” IgG activity as determined by suppression of FcϵRI-dependent basophil histamine release [Niederberger V et al., Proc Natl Acad Sci USA 2004, 101: 14677-14682] and/or inhibition of FcϵRII (CD23)-dependent binding of IgE-allergen complexes to B cells seems to offer a better prediction of the individual clinical response (Wacholz P A et al., J Allergy Clin Immunol 2003; 112: 915-922).

Allergen-specific immunotherapy can modulate different components of the immune system. Cellular modifications consist of a reduction in allergen-induced T-cell proliferation, indicating the induction of peripheral tolerance in allergen-specific T cells and a decrease in antigen-specific Th2-dominated immune response in favor of a Th1 reaction with increased IFN-γ production (Durham S R et al., J Allergy Clin Immunol 1996, 97: 1356-1365). The key cell type responsible for coordinating this immunological switch is a heterogeneous T-cell population, called regulatory T cells (T_(reg)). At the cellular level, the crucial factor for successful allergen immunotherapy is the peripheral induction of type 1 T_(reg) cells. Functional studies on type 1 T_(reg) cells, specific in recognizing antigens, revealed that the modulation of Th1 and Th2 responses by type 1 T_(reg) cells mostly depends on the secretion of the cytokine IL-10, which has immunosuppressive properties. In fact, IL-10 inhibits the proliferative response of peripheral T cells against specific allergens and plays a central role in the induction of T-cell anergy (James L K, Durham S R, Clin Exp Allergy 2008, 38: 1074-1088). In vitro, IL-10 enhances the expression of the regulatory factor FoxP3, modulates eosinophilic function and reduces pro-inflammatory mediators released by mast cells (Mobs C, et al., Int Arch Allergy Immunol 2008, 147: 171-178).

Another possible marker of the outstanding clinical efficacy of said iMAT molecules-mediated immunotherapy is the detection of changes in the number or the nature of allergen-specific T cells. On the basis of, for example, Bet v1 tetramer staining studies, the levels and characteristics of circulating birch pollen-specific CD4⁺ T cells can potentially be compared before and after SIT (van Overtvelt L et. al., J Immunol 2008, 180: 4514-4522). Recently, transforming growth factor (TGF)-β has also been identified as a key cytokine in successful SIT. Many actions may account for its relevance, such as the suppression of specific Th1, Th2 and Th17 cells, the induction of FoxP3 and the suppressive function of Tregs. In addition, TGF-β down regulates FcϵRI expression on Langherhans cells and suppresses IgE synthesis (Akdis C A, Akdis M J, Allergy Clin Immunol 2009, 123: 735-746).

Example 5—Comparison of iMAT Molecules According to the Present Invention with Prior Art MAT Molecules According to WO 2004/035793 (US Equivalent US 2005/0281816)

For assessment of purity of a MAT protein, a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) test procedure has been established (Thompson J et al., J Biol Chem 2002, 277: 34310-34331). The method, including sample preparation with a reducing agent, Lithium Dodecylsulfate (LDS) and heating at 75° C., resulted in reproducible multiple sharp bands after electrophoretic separation. Staining with Coomassie blue gives linear quantitative (densitometry) features in gels loaded with 200 to 1000 μg protein. Using a monoclonal antibody, detecting the allergen module in a MAT molecule with Fel d 1 as allergen module (MAT-Fel d1) it has been shown, that the main band and 13 minor bands all contain the MAT-Fel d1 protein. The small bands migrate at the same position as on the original gel also after re-loading on the gel (FIGS. 2A and 2B). Several different methods, such as different temperature and buffer composition protocols, for sample preparation prior to PAGE generated the same band pattern.

In all of these bands the presence of the full length (complete) MAT-Fel d1 protein and only traces of host cell proteins could be demonstrated after each band was cut out of the gel, digested by trypsin and subsequently analyzed by mass spectrometry (nanoLC/ESI-MS). From these experiments an anomalous feature (gel shifting), e.g., of different folding variants, of MAT-Fel d1 in the SDS-PAGE can be concluded. This means that MAT-Fel d1 in the analyzed preparation is not suitable as biopharmaceutical molecule, in particular for clinical and/or commercial biopharmaceutical manufacturing, since its purity could not be determined with standard methods (e.g. SDS-PAGE), but only with the modified procedure explained above.

In contrast to this gel shifting phenomenon of the MAT-Fel d1 molecule, the Fel d1 as such does not show such anomalous feature in SDS PAGE (FIG. 3, lanes 2 and 3). The Fel d1 displays a single sharp band at the expected molecular weight (19.6 kD).

A further anomalous feature could be observed in RP-HPLC analysis. No single peak of the MAT-Fel d1 was seen in this analytical method (FIG. 4), neither in the native conformation of the protein nor in the denatured form induced by chaotropic and reducing conditions. However, for GMP certified biopharmaceutical manufacturing a single isoform of the biomolecule in marketed pharmaceutical preparations is mandatory.

These observations in SDS-PAGE and RP-HPLC analysis may be explained by the physicochemical properties based on the amino acid sequence. Analysis in the Kyte & Doolittle hydrophobicity plot [Kyte J, Doolittle R F, Journal of Molecular Biology 1982, 157(1), 105-132] revealed adjacent extreme hydrophobic and hydrophilic domains (FIG. 5) which may be responsible for this anomalous behavior.

In particular the hydrophobic region of the targeting domain of the fusion protein is similar to the transmembrane segments of membrane proteins which are known in the art to cause such anomalous feature [Rath A et al., Proc Natl Acad Sci USA. 2009, 106(6): 1760-1765].

Migration on SDS-PAGE, that does not correlate with formula's molecular weights, termed “gel shifting” appears to be common for membrane proteins. This means, that the prerequisite of the SDS-PAGE method, which is a separation of molecules solely according to their molecular weight, independent on their native 2D- or 3D-structure does not apply in these cases. In the above cited work (PNAS article), the authors investigate the anomalous gel mobility of helical membrane proteins using a library of wild-type and mutant helix-loop-helix (“hairpin”) sequences derived from transmembrane segments 3 and 4 of the human cystic fibrosis transmembrane conductance regulator (CFTR), including disease-phenotypic residue substitutions. They found that these hairpins migrate at rates of minus 10% to plus 30% vs. their actual formula's molecular weights on SDS-PAGE and load detergent at ratios ranging from 3.4-10 g SDS/g protein. They additionally demonstrated that mutant gel shifts strongly correlate with changes in hairpin SDS loading capacity, and with hairpin helicity, indicating that gel shift behavior originates in altered detergent binding. In some cases, this differential solvation by SDS may result from replacing protein-detergent contacts with protein-protein contacts, implying that detergent binding and folding are intimately linked.

The SDS PAGE (FIG. 6) as well as the RP-HPLC analysis (FIG. 4 and FIG. 7) of MAT and iMAT proteins revealed substantial differences in the migration pattern or elution, respectively. The oxidized form of MAT-Fel d1 did not show a single sharp band on the SDS-PAGE gel (Lane 3) but several diffuse bands with larger and smaller apparent molecular weights than the actual 32.2 kD of MAT-Fel d1. In contrast iMAT-Cul o4 exhibited a single sharp band (M=41.6 kD) under oxidized conditions. Also the RP-HPLC chromatogram showed a single peak (FIG. 7).

Under reducing conditions the MAT-Fel d1 in the SDS-PAGE reveals a main band migrating approximately at the known molecular weight but in addition some of the minor bands described in FIGS. 2A and 2B known to contain the complete sequence of MAT-Fel d1 emerge again (FIG. 6, lane 6). This is an attribute, which is characteristic for the anomalous feature of MAT-Fel d1. Additionally the RP-HPLC chromatogram of MAT-Fel d1 under reducing conditions (FIG. 4, right graph) exhibit at least 3 different isotypes of the MAT-Fel d1. In contrast the iMAT molecules reveal characteristics evidently indicative for a single isotype in the SDS-PAGE (FIG. 6, lane 7) as well as in the RP-HPLC (FIG. 7).

The reducing conditions lead to a cleavage of the disulfide bridges in the MAT molecule, thus the MAT and the iMAT molecules should behave alike under reducing conditions if the disulfide bridges are solely responsible for the anomalous feature of MAT. However, this is not the case, since the anomalous gel shifting and the occurrence of isoforms in RP-HPLC of MAT molecules is still present under reducing conditions.

However, the iMAT molecule does not show such gel shifting and exhibits a peak in RP-HPLC chromatogram in the native (oxidized) form of the protein. Furthermore the Kyte-Doolittle plots (Kyte, J. and Doolittle, R. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132) of MAT and iMAT molecules are nearly identical at the N-terminus covering the sequence of His-tag, TAT and targeting domain (FIG. 11). Consequently, a person skilled in the art would not be motivated to construct a MAT molecule according to the prior art with cysteine residues substituted with other amino acid residues in order to overcome the disadvantages of the prior art.

The three yielded iMAT molecules have been constructed by the “bioinformatical engineering” procedures according to Example 6 below and produced by recombinant expression technology in E. coli. All three iMAT molecules were stable in buffer (20 mM citrate, 1 M arginine, pH 6.0) after freezing and thawing twice and could be adsorbed to ADJU-PHOS® (Brenntag, Denmark) as adjuvant, so that the iMAT molecules can be used as a vaccine. The proteins could be desorbed from ADJU-PHOS® without degradation in the same buffer system (FIG. 9).

Example 6—“Bioinformatical Engineering” of iMAT Molecules for Targeting IBH in Equines

In order to, for example, treat horses with allergic insect bite hypersensitivity (IBH) using the iMAT technology effectively, it is further mandatory:

-   -   a. to select a culicoides protein as allergen module in iMAT         molecules that is a major allergen and thus has a high         prevalence to cause hypersensitivity in affected horses and thus         can also be the target for tolerance induction, and     -   b. to construct an iMAT molecule with said major allergens that         is thermodynamically stable and can be produced efficiently by         protein engineering and can additionally be analyzed with         standard methods to ensure sufficient enough quality (i.e.,         identity, purity and potency).

In order to fulfil these requirements, a bioinformatics approach was chosen for the selection of the allergen to be included into the iMAT molecules according to the invention. The objective of the selection was (i) to choose one or more allergens to be expected to be of relevance in IBH, i.e., that the majority of horses suffering from IBH are sensitized to the respective allergen, and (ii) to choose the allergen with the highest probability of comprising linear epitopes of allergen characteristics, i.e., comprising high numbers of short peptide sequences (7 to 13 amino acid residues) homologue to those in published allergens.

Currently approximately 230 proteins from culicoides (Culicoides sonorensis, Culicoides nubeculosus, Culicoides obsoletus) found in saliva are known that might potentially elicit allergies in subjects, e.g., equines. To select appropriate antigens for pharmaceutical preparations, a homology comparison based on local sequence alignments to known non-culicoides allergens was chosen. Often epitope detection for antibody recognition (mostly conformational epitopes) is achieved by functional analysis (e.g., peptide microarrays) or for T-cells epitopes (linear epitopes) by calculation of peptide binding probabilities to MHC molecules. The therapeutic principle of the iMAT technology inter alia is based on endocytosis and degradation by acid-dependent proteases in endosomes followed by MHC Class II binding and antigen presentation. In equines, the characteristics of such systems are currently not fully explored since the allelic diversity of the equine MHC genes is far less investigated as compared to the human system and thus experimentally not readily available. Furthermore the research on IBH as a Type I allergy and the causal allergens eliciting the symptoms has only recently started. The first protein characterized as allergen active in effector cells (i.e., basophil granulocytes) was not described until 2008 [Langner et al., Vet Immunol Immunopathol 2008, 122(1-2):126-137].

Thus a different—non experimental but bioinformatics—approach for allergen selection was chosen that is based on local homology searches of peptides derived from culicoides proteins to known non-culicoides allergenic proteins, most of which are known to raise allergies in humans. Amino acid sequences of proteins suspected to have allergenic properties were exported from publicly available databases (e.g., UNIPROT) and redundancies were determined by analysis of sequences homologies within the exported dataset. Highly homologue sequence counterparts were eliminated and the resulting remainder of sequences served as the canonical sequence database of probable valid antigens for subsequent analyses. To determine culicoides proteins with putative high allergenic potential, proteins were in silico cleaved into peptides with lengths of 6 to 15 amino acids with a one amino acid shifting. Next local-pairwise alignments of each culicoides protein and the corresponding peptides to the canonical sequence database were performed. Following this, a scaling of obtained alignment hits was conducted by setting the self-alignment score of a given culicoides protein to one and alignment hits of the corresponding peptides accordingly. Next the number of alignment hits exceeding a given threshold were counted for each peptide and compared by local-pairwise alignment to a randomly generated database of protein sequences with no known allergenic properties, and subsequently scaled and counted. The resulting “non allergic protein” counts were subtracted from those of the allergen results and cumulative hit scores for each culicoides protein based on the number of hits for all corresponding peptides were calculated (FIG. 12). Proteins with highest counts were selected as iMAT antigen module candidates.

For validation of the bioinformatic antigen selection method the occurrence of sensitization against five culicoides allergens in 13 horses suffering from clinically diagnosed IBH was measured. All selected antigens were tested in a semi-quantitative functional ex vivo experiment based on the allergen specific histamine release from equine basophiles isolated from blood samples (Histamine Release Test=HRT, details of the assay: see Example 2). The recombinant allergens were tested in 3 concentrations and the score value for each allergen ranged between 0 (no sensitization) to 6 (highest sensitization). The data from all 13 horses were compared to the results of the bioinformatics calculations (FIG. 8). This analysis shows an excellent overall correlation (r=0.97) between the sensitization (total score values per allergen of the cohort) and the prediction score. From this correlation analysis we conclude that the bioinformatics antigen selection method is suitable to select relevant culicoides allergens for the antigen module in iMAT molecules. Thus, the IBH affected horses can be treated with iMAT molecules according to the present invention comprising the selected allergens in order to induce tolerance against these allergens with high probability in a large proportion of the subgroup of diseased subjects.

Three allergens have been selected based on the bioinformatics analysis to be included in three different iMAT molecules, i.e., Cul o3, Cul o2 and Cul o4.

Each of the selected allergens were integrated into separate iMAT molecules as the antigen module and subsequently optimized for thermodynamic stability by iterative modeling of three-dimensional protein structures and calculation of changes of free energies after substitution of single amino acids. Physicochemical properties and stability is influenced by substituting different amino acid residue(s) within the primary amino acid sequence.

The results of the herein described analyses (antigen search and modeling) were transformed into an iMAT amino acid sequence suitable for pharmacological production and application in equines in order to treat e.g., IBH.

Example 7—Construction of Mosaic-Like iMAT Molecules According to the Invention

It is expected that iMAT molecules according to the invention can further be improved if components of more than one allergen are included into the antigen module. For this purpose it is possible to apply the basic principle of the above described bioinformatics selection approach (Example 6) in a different way. Instead of selecting complete allergens based on the hit count of allergen peptides found in the allergen data base, only the most abundant peptides of several of such allergens are used to engineer an iMAT antigen module. Thus, such an iMAT molecule consists of an antigen module of peptides that stem from several allergens. This allows broadening of the spectrum of a single iMAT molecule with respect to its targeted allergic profile and is thus beneficial for pharmacological drug development.

In order to find short peptide sequences that qualify for such mosaic-like iMAT protein 230 proteins from Culicoides species (Culicoides sonorensis, Culicoides nubeculosus, Culicoides obsoletus) found in saliva were analyzed by homology comparison as described above (see Example 6). Briefly in silico cleaved Culicoides proteins with peptide lengths of 6-15 amino acid residues were locally aligned to a canonical sequence database of allergen-related proteins and a random database of non-allergy-related proteins. The number of differences of significant homologies for each peptide found within the canonical database was determined. Subsequently, each peptide was locally aligned to a random database triple the size of the canonical database to reduce false positive hits. The top (e.g., tenth percentile) of remaining homologies for each peptide length is especially suitable to serve as a base for construction of a mosaic-like or hybrid allergen carrying iMAT molecule. To construct a mosaic-like iMAT molecule a protein precursor is chosen (for example, from the list of precursor proteins corresponding to top ranking peptides) as a scaffold protein for embedding top ranking peptides. The signal peptide sequence is removed from the scaffold protein and top ranking peptides with additional adjacent N- or C-terminal amino acids may be inserted within the original sequence of the scaffold protein or may replace parts of the original sequence of the scaffold protein. The position for insertion or replacement is determined using similarity alignments or the reference position of the peptide in the corresponding precursor protein. As a next step, His-Tag, the TAT and targeting domain are added. Finally cysteine residues are replaced by most stabilizing residues as described above.

In an exemplary instance of this approach a salivary protein of Culicoides sonorensis (UniProt database entry “Q66U13”) was used as a scaffold protein. The most allergenic structure within the protein was determined in order to conserve this part of the sequence. The signal peptide sequence is removed and subsequently sequences from UniProt database entries “Q5QBI9”, “Q5QBK6”, “Q5QBL6”, “Q5QBJ4” and “Q5QBI2” are added. Afterwards, the mosaic-like allergen is integrated into the iMAT general molecule structure. Finally, cysteine residues are replaced by other amino acid residues, preferably serine, leucine, isoleucine and/or aspartic acid that do not derogate the stability of the constructed iMAT molecule (fusion protein).

SEQ ID NO: 17 depicts the whole sequence of an exemplary mosaic-like (hybrid) iMAT molecule according to the present invention [Amino acid residue 1: N-terminal methionine, amino acid residues 2-7: His-tag, amino acid residues 8-18: TAT sequence, amino acid residues 19-128: targeting domain, amino acid residues 129-333: hybrid allergen (scaffold protein Q66U13 without signal peptide and inserted/replaced sequences; inserted/replaced sequences: amino acid residues 137-151: Q5QBI9; amino acid residues 155-166: Q66U13; amino acid residues 185-200: Q5QBK6; amino acid residues 215-229: Q5QBL6: amino acid residues 235-250; Q5QBL6; amino acid residues 265-278: Q5QBJ4; amino acid residues 318-333: Q5QBI2; substituted cysteines (serine): 46, 146, 158, 173, 222, 225, 246, 273, 283, 329; substituted cysteines (leucine): 295; substituted cysteines (isoleucine): 299; substituted cysteines (aspartic acid): 181].

Example 8—Therapeutic Vaccine/Prophylaxis of Recurrent Airways Obstruction (RAO) in Equines

A single iMAT molecule or a combination of iMAT molecules containing different antigen modules according to the present invention can be employed for treating prophylactically or therapeutically a horse suffering from or being at risk of RAO and/or summer pasture associated RAO. In horses iMAT molecules according to the present invention may be administered as described in Example 4.

Adult horses with a known history of RAO will be employed. Prior to the treatment, horses are conditioned e.g., to stand in stocks wearing a face-mask to enable a complete physical airway examination, including pneumotachograph measurements, upper airway endoscopy and bronchoalveolar lavage (BAL) for analysis of e.g., percent of neutrophils in BAL fluid. Complete blood count and biochemistry profile are performed to exclude the presence of concomitant medical conditions.

The following parameters may be investigated to examine the respiratory system and to measure efficacy of a therapeutic and/or prophylactic treatment with iMAT molecules: change in lung function variables e.g., respiratory rate, maximal transpulmonary pressure, lung resistance, and/or lung elastance. Additionally, the parameter may be incorporated into a weighted clinical scoring system e.g. also evaluating clinical scores of breathing effort/abdominal lift, nasal discharge and/or flaring, cough and/or abnormal lung, bronchial and/or tracheal sounds.

Thus, throughout the treatment period and/or thereafter the efficacy of a therapy or the prevention of RAO can be investigated clinically by quantitative, semi-quantitative or qualitative assessments.

These clinical parameters may be compared to clinical signs of the individual horse in previous seasons and/or to the severity prior to the start of a therapeutic intervention. Alternatively, a comparison to RAO affected horses that are not treated or treated with placebo may demonstrate the efficacy of the iMAT molecule-mediated treatment and/or prevention of clinical signs of RAO.

Bronchoalveolar lavage (BAL) fluid and/or fresh blood of said horses may be used in an in vitro provocation test for type 1 allergic reactions in horses, e.g., with HRT or CAST® (for details, see Example 2 and/or Hare et al Can J Vet Res 1998; 62: 133-139). A reduced pulmonary mast cell and/or basophil degranulation in response to a challenge with certain allergens, e.g., histamine and/or sulfidoleukotriene release after the iMAT molecule treatment as compared to before, indicate a therapy and/or prevention effect.

Alternatively or in addition, employing certain recombinant allergens an intradermal provocation test, skin prick test or also allergen specific IgE and/or IgG determination in BAL fluid or serum may be monitored in said horses (Tilley P et al., J Equine Vet Sci 2012, 32: 719-727). A reduced response (immediate and/or late phase reactivity) and/or changes of the antibody titers indicate a therapy and/or prevention effects of the iMAT molecule treatment.

REFERENCES

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IN THE SEQUENCE LISTING

SEQ ID NO: 1 relates to a suitable minimal amino acid sequence for one translocation module according to the present invention which is still being functional, i.e., capable of effectively promoting cell entry;

SEQ ID NO: 2 relates to the full equine invariant chain amino acid sequence;

SEQ ID NO: 3 relates to the full Cul n4 allergen amino acid sequence;

SEQ ID NO: 4 relates to the full Cul o1 allergen amino acid sequence;

SEQ ID NO: 5 relates to the full Cul o2 allergen amino acid sequence;

SEQ ID NO: 6 relates to the full Cul o3 allergen amino acid sequence;

SEQ ID NO: 7 relates to a Cul n4 iMAT molecule according to the present invention;

SEQ ID NO: 8 relates to a Cul n4 iMAT molecule according to the present invention;

SEQ ID NO: 9 relates to a Cul o1 iMAT molecule according to the present invention;

SEQ ID NO: 10 relates to a Cul o1 iMAT molecule according to the present invention;

SEQ ID NO: 11 relates to a Cul o2 iMAT molecule according to the present invention;

SEQ ID NO: 12 relates to a Cul o2 iMAT molecule according to the present invention;

SEQ ID NO: 13 relates to a Cul o3 iMAT molecule according to the present invention;

SEQ ID NO: 14 relates to a Cul o3 iMAT molecule according to the present invention;

SEQ ID NO: 15 relates to a specific fragment of the equine invariant chain amino acid sequence with maintained intracellular transport function;

SEQ ID NO: 16 relates to a specific fragment of the equine invariant chain amino acid sequence with maintained intracellular transport function;

SEQ ID NO: 17 relates to the whole sequence of an exemplary mosaic-like iMAT molecule according to the present invention;

SEQ ID NO: 18 relates to the full Cul o4 allergen amino acid sequence;

SEQ ID NO: 19 relates to the full Cul o7 allergen amino acid sequence;

SEQ ID NO: 20 relates to a Cul o4 iMAT molecule according to the present invention;

SEQ ID NO: 21 relates to a Cul o4 iMAT molecule according to the present invention;

SEQ ID NO: 22 relates to a Cul o7 iMAT molecule according to the present invention;

SEQ ID NO: 23 relates to a Cul o7 iMAT molecule according to the present invention.

All prior art references cited herein as well as the sequence listing accompanying this application are hereby independently from each other incorporated by reference in their entirety. 

What is claimed is:
 1. An improved modular antigen transportation (iMAT) molecule, comprising: a) at least one first module being an amino acid sequence allowing the translocation of the iMAT molecule from the extracellular space into the interior of cells, b) at least one second module being an amino acid sequence allowing species-specific intracellular targeting of the iMAT molecule to the cell organelles which are involved in the processing of antigens and/or the loading of MHC molecules with antigens, and c) at least one third module as antigen module being a specific amino acid sequence that allows modulating the immune response against an epitope of an antigen or an antigen and determining the specificity of the immune response in a subject, wherein said antigen module(s) comprise(s) at least one cysteine residue that is substituted with a different amino acid residue.
 2. The iMAT molecule according to claim 1, wherein said cysteine residue is substituted with serine, leucine, isoleucine, aspartic acid, or combinations thereof.
 3. The iMAT molecule according to claim 1, wherein in the at least one antigen module all cysteine residues are substituted with a different amino acid residue.
 4. The iMAT molecule according to claim 3, wherein said cysteine residue is substituted with serine, leucine, isoleucine, aspartic acid, or combinations thereof.
 5. The iMAT molecule according to claim 1, wherein in the entire iMAT molecule all cysteine residues are substituted with a different amino acid residue.
 6. The iMAT molecule according to claim 5, wherein said cysteine residue is substituted with serine, leucine, isoleucine, aspartic acid, and combinations thereof.
 7. The iMAT molecule according to claim 1, wherein all of such modules are covalently linked to each other.
 8. The iMAT molecule according to claim 7, wherein said iMAT molecule further comprises spacer modules between each module.
 9. The iMAT molecule according to claim 7, wherein said iMAT molecule comprises spacer modules between each of such first, second and third modules in the iMAT molecule.
 10. The iMAT molecule according to claim 7, wherein the iMAT molecule does not comprise spacer modules between two or more adjacent modules.
 11. The iMAT molecule according to claim 1, wherein the at least one second module comprises the equine invariant chain.
 12. The iMAT molecule according to claim 1, wherein the at least one second module comprises one or more of the amino acid sequences of SEQ ID NOS: 2, 15, or
 16. 13. The iMAT molecule according to claim 1, wherein the at least one antigen module comprises at least one full or partial epitope derived from at least one allergen eliciting an allergy in equines.
 14. The iMAT molecule according to claim 13, wherein at least one full or partial epitope of at least one allergen is derived from blood feeding insects.
 15. The iMAT molecule according to claim 14, wherein said blood feeding insects are from the genus Culicoides.
 16. The iMAT molecule according to claim 13, wherein said allergen is derived from mold, fungi, fungi spores, pollen, house dust, forage mites, or forage mite feces.
 17. The iMAT molecule according to claim 16, wherein pollen is selected from the group consisting of tree, grass, herbaceous, ambrosia or brassicaceae pollen.
 18. The iMAT molecule according to claim 16, wherein said mold, fungi and/or spores are selected from the genera Aspergillus, Alternaria, Botrytis, Cercospora, Cladosporium, Curvularia, Drechslera, Eurotium, Helminthosporium, Epicoccum, Erysiphe/Oidium, Fusarium, Lichtheimia, Nigrospora, Penicillium, Periconia, Peronospora, Polythrincium, Stemphylium, Torula and combinations thereof.
 19. The iMAT molecule according to claim 16, where said forage mite or forage mite feces are selected from the genera Acarus, Glycophagus, Tyrophagus, Dermatophagoides and combinations thereof.
 20. The iMAT molecule according to claim 12, wherein such at least one antigen is selected from Cul n4, Cul o1, Cul o2, Cul o3, Cul o4 and/or Cul o7.
 21. The iMAT molecule according to claim 1, wherein the at least one antigen module comprises at least one full or partial epitope derived from at least one antigen of a pathogen eliciting one or more infectious disease(s) in equines.
 22. The iMAT molecule according to claim 21, wherein the at least one antigen module comprises at least one full or partial epitope derived from at least one antigen is selected from the genera Rhodococcus, Streptococcus, Orbivirus, Flavivirus, Trichophyton, Microsporum, Cryptosporidium, Strongylus, and combinations thereof.
 23. The iMAT molecule according to claim 22, wherein the at least one antigen module also comprises an antigen of a vector involved in the transmission of one or more infectious diseases in equines.
 24. The iMAT molecule according to claim 23, wherein said antigen of a vector is selected from Culicoides, Culex and/or Ixodes saliva components.
 25. The iMAT molecule according to claim 1, further comprising at least one tag module.
 26. The iMAT molecule according to claim 25, wherein said tag module comprises at least one His-tag.
 27. The iMAT molecule according to claim 25, wherein such at least one tag module is present at the N-terminus and/or at the C-terminus, together with one or more adjacent amino acid residues.
 28. The iMAT molecule according to claim 25, wherein said at least one tag module is present N-terminally after one methionine residue.
 29. The iMAT molecule according to claim 1, wherein the at least one first module comprises the amino acid sequence of HIV-tat, VP22 and/or Antennapedia or a partial sequence thereof.
 30. The iMAT molecule according to claim 1 being present in monomeric form and/or linear form.
 31. The iMAT molecule according to claim 1 comprising one or more of the amino acid sequences according to SEQ ID NOS: 7, 8, 9, 10, 11, 12, 13, 14, 17, 20, 21, 22, or
 23. 32. An immunogenic composition comprising the iMAT molecule according to claim
 1. 33. The iMAT molecule according to claim 29, wherein the at least one first module comprises the amino acid sequence according to SEQ ID NO:
 1. 